diff options
Diffstat (limited to 'metadata/md5-cache/sci-biology')
200 files changed, 0 insertions, 2428 deletions
diff --git a/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 deleted file mode 100644 index 0ac48a6b6a87..000000000000 --- a/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=app-arch/unzip -DESCRIPTION=A Plasmid Editor -EAPI=5 -HOMEPAGE=http://www.biology.utah.edu/jorgensen/wayned/ape/ -KEYWORDS=~amd64 ~x86 -LICENSE=ApE -RDEPEND=dev-lang/tcl:0 dev-lang/tk:0 -RESTRICT=mirror -SLOT=0 -SRC_URI=http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ApE-2.0.7.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=bf78ab8abbdb34e4f7d5c8a0b4429c0f diff --git a/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 deleted file mode 100644 index a6f09e576320..000000000000 --- a/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install postinst prepare prerm setup test unpack -DEPEND=dev-perl/Module-Build dev-perl/Capture-Tiny !<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 -DESCRIPTION=Generic Model Organism Database Project - The Generic Genome Browser -EAPI=5 -HOMEPAGE=http://gmod.org/wiki/GBrowse -IUSE=-minimal mysql postgres +sqlite vhosts -KEYWORDS=~amd64 ~x86 -LICENSE=|| ( Artistic GPL-1+ ) -RDEPEND=!<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 -SLOT=0 -SRC_URI=mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.48.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 6ae2395d7f341093c36057cb4f69101a -_md5_=bccaeef3292f6df307fc14fb5a2a74b2 diff --git a/metadata/md5-cache/sci-biology/HTSeq-0.9.1 b/metadata/md5-cache/sci-biology/HTSeq-0.9.1 deleted file mode 100644 index 7258648c3877..000000000000 --- a/metadata/md5-cache/sci-biology/HTSeq-0.9.1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files -EAPI=6 -HOMEPAGE=https://htseq.readthedocs.io/ -IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 -KEYWORDS=~amd64 -LICENSE=GPL-3+ -RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) -SLOT=0 -SRC_URI=mirror://pypi/H/HTSeq/HTSeq-0.9.1.tar.gz -_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=baebb3e5c138076f90cdaad5bc41573f diff --git a/metadata/md5-cache/sci-biology/HTSeq-9999 b/metadata/md5-cache/sci-biology/HTSeq-9999 deleted file mode 100644 index a32fe245b1ad..000000000000 --- a/metadata/md5-cache/sci-biology/HTSeq-9999 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-vcs/git-1.8.2.1[curl] -DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files -EAPI=6 -HOMEPAGE=https://htseq.readthedocs.io/ -IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 -LICENSE=GPL-3+ -RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) -SLOT=0 -_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 git-r3 8f6de46b0aa318aea0e8cac62ece098b multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=baebb3e5c138076f90cdaad5bc41573f diff --git a/metadata/md5-cache/sci-biology/Manifest.gz b/metadata/md5-cache/sci-biology/Manifest.gz Binary files differdeleted file mode 100644 index 69dcc4eee699..000000000000 --- a/metadata/md5-cache/sci-biology/Manifest.gz +++ /dev/null diff --git a/metadata/md5-cache/sci-biology/STAR-2.5.3a b/metadata/md5-cache/sci-biology/STAR-2.5.3a deleted file mode 100644 index 42bf0cc5cf13..000000000000 --- a/metadata/md5-cache/sci-biology/STAR-2.5.3a +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install pretend setup -DEPEND=sci-libs/htslib:= virtual/pkgconfig -DESCRIPTION=STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays -EAPI=6 -HOMEPAGE=https://github.com/alexdobin/STAR -KEYWORDS=~amd64 -LICENSE=GPL-3 -RDEPEND=sci-libs/htslib:= -SLOT=0 -SRC_URI=https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz -> STAR-2.5.3a.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=1eb821b9192887ab1f2ac6b1536037ac diff --git a/metadata/md5-cache/sci-biology/aaindex-9.1-r1 b/metadata/md5-cache/sci-biology/aaindex-9.1-r1 deleted file mode 100644 index 618805eb016b..000000000000 --- a/metadata/md5-cache/sci-biology/aaindex-9.1-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( sci-biology/emboss ) -DESCRIPTION=Amino acid indices and similarity matrices -EAPI=6 -HOMEPAGE=https://www.genome.jp/aaindex/ -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=emboss? ( sci-biology/emboss ) -SLOT=0 -SRC_URI=mirror://gentoo/aaindex-9.1.tar.bz2 -_md5_=8636229aaffdb1c6d95611b06d3cd161 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 b/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 deleted file mode 100644 index a3fd873fbd89..000000000000 --- a/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure prepare pretend setup -DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc dev-haskell/mmap ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -EAPI=6 -HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ -IUSE=+mpi openmp misc-haskell -KEYWORDS=~amd64 ~x86 -LICENSE=abyss -RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) -SLOT=0 -SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz -> abyss-2.0.2.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=3b173739bd4e2f9d61a49918b3b8bc05 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.3 b/metadata/md5-cache/sci-biology/abyss-2.0.3 deleted file mode 100644 index 9b3eb150625c..000000000000 --- a/metadata/md5-cache/sci-biology/abyss-2.0.3 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure prepare pretend setup -DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -EAPI=6 -HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ -IUSE=+mpi openmp misc-haskell -KEYWORDS=~amd64 ~x86 -LICENSE=abyss -RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) -SLOT=0 -SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.3.tar.gz -> abyss-2.0.3.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=4c70cbdf60d5dc2d564272b103f2b469 diff --git a/metadata/md5-cache/sci-biology/allpathslg-52488-r2 b/metadata/md5-cache/sci-biology/allpathslg-52488-r2 deleted file mode 100644 index 375f587d3cbf..000000000000 --- a/metadata/md5-cache/sci-biology/allpathslg-52488-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare pretend setup -DEPEND=!sci-biology/allpaths !sci-biology/vaal dev-libs/boost:= >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=De novo assembly of whole-genome shotgun microreads -EAPI=6 -HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd -KEYWORDS=~amd64 -LICENSE=MIT -RDEPEND=!sci-biology/allpaths !sci-biology/vaal -SLOT=0 -SRC_URI=ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz https://dev.gentoo.org/~mgorny/dist/allpathslg-52488-patchset.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=8c8bda5ab2704db1e969660ebe5882c1 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r3 b/metadata/md5-cache/sci-biology/amap-2.2-r3 deleted file mode 100644 index 9f4a18e85342..000000000000 --- a/metadata/md5-cache/sci-biology/amap-2.2-r3 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install preinst prepare setup -DEPEND=java? ( >=virtual/jdk-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 ) -DESCRIPTION=Protein multiple-alignment-based sequence annealing -EAPI=6 -HOMEPAGE=http://bio.math.berkeley.edu/amap/ -IUSE=java elibc_FreeBSD java elibc_FreeBSD -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=java? ( >=virtual/jre-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) -SLOT=0 -SRC_URI=http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-opt-2 77d2e22d0de7640f817d20e861c0ff3f java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=6bd792e8b76c06ee993b88f83e48b907 diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0-r4 b/metadata/md5-cache/sci-biology/amos-3.1.0-r4 deleted file mode 100644 index 4371af713ae7..000000000000 --- a/metadata/md5-cache/sci-biology/amos-3.1.0-r4 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install prepare setup -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A Modular, Open-Source whole genome assembler -EAPI=6 -HOMEPAGE=http://amos.sourceforge.net/ -IUSE=python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-perl/DBI dev-perl/Statistics-Descriptive sci-biology/mummer -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=mirror://sourceforge/amos/amos-3.1.0.tar.gz https://dev.gentoo.org/~soap/distfiles/amos-3.1.0-fix-c++14.patch.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=aec6d1c76d5ea621c66e803800e2b3c4 diff --git a/metadata/md5-cache/sci-biology/arb-6.0.6 b/metadata/md5-cache/sci-biology/arb-6.0.6 deleted file mode 100644 index 8fd630306977..000000000000 --- a/metadata/md5-cache/sci-biology/arb-6.0.6 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile install prepare test unpack -DEPEND=app-text/sablotron media-libs/libpng:= media-libs/tiff:= www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew:= media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sys-process/time x11-misc/makedepend -DESCRIPTION=Tools for DNA/RNA sequence database handling and phylogenetic analysis -EAPI=6 -HOMEPAGE=http://www.arb-home.de/ -IUSE=debug +opengl test -KEYWORDS=~amd64 ~x86 -LICENSE=arb -RDEPEND=app-text/sablotron media-libs/libpng:= media-libs/tiff:= www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew:= media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sci-visualization/gnuplot -RESTRICT=debug? ( test ) -SLOT=0 -SRC_URI=http://download.arb-home.de/release/arb-6.0.6/arb-6.0.6-source.tgz -> arb-6.0.6.tgz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=c13fb556a26877506fa69c3a46586bbd diff --git a/metadata/md5-cache/sci-biology/ariadne-1.3-r3 b/metadata/md5-cache/sci-biology/ariadne-1.3-r3 deleted file mode 100644 index b27761ea4fe5..000000000000 --- a/metadata/md5-cache/sci-biology/ariadne-1.3-r3 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 -DESCRIPTION=Protein sequences and profiles comparison -EAPI=6 -HOMEPAGE=http://www.well.ox.ac.uk/ariadne/ -IUSE=static-libs -KEYWORDS=~amd64 ~x86 -LICENSE=ARIADNE -RDEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 -SLOT=0 -SRC_URI=http://www.well.ox.ac.uk/ariadne/ariadne-1.3.tar.Z -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=a99266aecef97d81f48df25aa43fbb4a diff --git a/metadata/md5-cache/sci-biology/augustus-2.5.5 b/metadata/md5-cache/sci-biology/augustus-2.5.5 deleted file mode 100644 index 4458afad6a1a..000000000000 --- a/metadata/md5-cache/sci-biology/augustus-2.5.5 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Eukaryotic gene predictor -EAPI=4 -HOMEPAGE=http://augustus.gobics.de/ -IUSE=examples -KEYWORDS=amd64 x86 -LICENSE=Artistic -SLOT=0 -SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=5660f556708e8c3b5d43c9ef832e66ec diff --git a/metadata/md5-cache/sci-biology/bamtools-2.5.1 b/metadata/md5-cache/sci-biology/bamtools-2.5.1 deleted file mode 100644 index 96eae69a4e21..000000000000 --- a/metadata/md5-cache/sci-biology/bamtools-2.5.1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test -DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= virtual/pkgconfig dev-util/ninja >=dev-util/cmake-3.9.6 -DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files -EAPI=6 -HOMEPAGE=https://github.com/pezmaster31/bamtools -IUSE=static-libs -KEYWORDS=~amd64 ~x86 -LICENSE=MIT -RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= -SLOT=0/2.5.1 -SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz -> bamtools-2.5.1.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=283ed3269c843bce2ee0a9cefad79fe0 diff --git a/metadata/md5-cache/sci-biology/bamtools-9999 b/metadata/md5-cache/sci-biology/bamtools-9999 deleted file mode 100644 index 29369b70bcf4..000000000000 --- a/metadata/md5-cache/sci-biology/bamtools-9999 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test unpack -DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= virtual/pkgconfig dev-util/ninja >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] -DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files -EAPI=6 -HOMEPAGE=https://github.com/pezmaster31/bamtools -IUSE=static-libs -LICENSE=MIT -RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= -SLOT=0/9999 -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=283ed3269c843bce2ee0a9cefad79fe0 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.5 b/metadata/md5-cache/sci-biology/bcftools-1.5 deleted file mode 100644 index e85ec2da4ff9..000000000000 --- a/metadata/md5-cache/sci-biology/bcftools-1.5 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] -DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files -EAPI=6 -HOMEPAGE=http://www.htslib.org -IUSE=python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=MIT -RDEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] -REQUIRED_USE=|| ( python_targets_python2_7 ) -SLOT=0 -SRC_URI=https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 -_eclasses_=multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=e289371e3fec376baf8fe36c652ca521 diff --git a/metadata/md5-cache/sci-biology/bedtools-2.26.0 b/metadata/md5-cache/sci-biology/bedtools-2.26.0 deleted file mode 100644 index 3f9bfd1ca054..000000000000 --- a/metadata/md5-cache/sci-biology/bedtools-2.26.0 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install setup -DEPEND=|| ( dev-lang/python:3.6 dev-lang/python:3.5 dev-lang/python:3.4 >=dev-lang/python-2.7.5-r2:2.7 ) test? ( sci-libs/htslib sci-biology/samtools:0 ) -DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats -EAPI=6 -HOMEPAGE=https://bedtools.readthedocs.io/ -IUSE=test -KEYWORDS=~x86 ~amd64 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib -SLOT=0 -SRC_URI=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz https://dev.gentoo.org/~mgorny/dist/bedtools-2.26.0-fix-buildsystem.patch.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=e072d90aa6492a70f261161c8d5551e5 diff --git a/metadata/md5-cache/sci-biology/bfast-0.7.0a b/metadata/md5-cache/sci-biology/bfast-0.7.0a deleted file mode 100644 index 21af40cfcc8e..000000000000 --- a/metadata/md5-cache/sci-biology/bfast-0.7.0a +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Blat-like Fast Accurate Search Tool -EAPI=5 -HOMEPAGE=https://sourceforge.net/projects/bfast/ -IUSE=test -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=dev-perl/XML-Simple -SLOT=0 -SRC_URI=mirror://sourceforge/bfast/bfast-0.7.0a.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=abc362f15c5107d96bedfb879ea0375f diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 deleted file mode 100644 index 100a03ec807f..000000000000 --- a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Multithreaded tool for matching large sets of patterns against biosequence DBs -EAPI=6 -HOMEPAGE=http://stephanopoulos.openwetware.org/BIOGREP.html -IUSE=doc examples -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://www.openwetware.org/images/3/3d/Biogrep-1.0.tar.gz -> biogrep-1.0.tar.gz doc? ( http://www.openwetware.org/images/4/49/Biogrep.pdf -> biogrep-1.0.pdf ) -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=9731727dae2a2514bcaa486b0059272e diff --git a/metadata/md5-cache/sci-biology/biopandas-0.2.1 b/metadata/md5-cache/sci-biology/biopandas-0.2.1 deleted file mode 100644 index 4c40d4cf9db7..000000000000 --- a/metadata/md5-cache/sci-biology/biopandas-0.2.1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] test? ( dev-python/nose[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -DESCRIPTION=Molecular Structures in Pandas DataFrames -EAPI=6 -HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/rasbt/biopandas https://pypi.org/project/BioPandas/ -IUSE=test python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=BSD -RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) -SLOT=0 -SRC_URI=mirror://pypi/B/BioPandas/biopandas-0.2.1.tar.gz -_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=ea88f22f7675491064ad08658a2ba291 diff --git a/metadata/md5-cache/sci-biology/bioperl-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-1.6.9 deleted file mode 100644 index 3de6735f1ef0..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-1.6.9 +++ /dev/null @@ -1,15 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] -DESCRIPTION=Perl tools for bioinformatics - Core modules -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=-minimal graphviz sqlite +db +network +run -KEYWORDS=amd64 x86 -LICENSE=|| ( Artistic GPL-1+ ) -PDEPEND=db? ( >=sci-biology/bioperl-db-1.6.9 ) network? ( >=sci-biology/bioperl-network-1.6.9 ) run? ( >=sci-biology/bioperl-run-1.6.9 ) -RDEPEND=dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] -REQUIRED_USE=minimal? ( !graphviz ) -SLOT=0 -SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=be22a76392a6e5c121e4b6d388045faa diff --git a/metadata/md5-cache/sci-biology/bioperl-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-9999-r1 deleted file mode 100644 index e17857bce202..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-9999-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/Set-Scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] dev-vcs/git -DESCRIPTION=Perl tools for bioinformatics - Core modules -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=-minimal graphviz +db +network +run -LICENSE=Artistic GPL-2 -PDEPEND=!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) db? ( >=sci-biology/bioperl-db-9999 ) network? ( >=sci-biology/bioperl-network-9999 ) run? ( >=sci-biology/bioperl-run-9999 ) -RDEPEND=dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/Set-Scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] -SLOT=0 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=210415961127105f0fc625670ba9e423 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 deleted file mode 100644 index 12bdb6098456..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl:=[-build(-)] -DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=test -KEYWORDS=amd64 x86 -LICENSE=|| ( Artistic GPL-1+ ) -RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] -RESTRICT=test -SLOT=0 -SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=2470d7ecf1b6ff1902a8d74057748480 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 deleted file mode 100644 index f2ddddec2bfb..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl:= -DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema -EAPI=6 -HOMEPAGE=http://www.bioperl.org/ -IUSE=test -KEYWORDS=~amd64 ~x86 -LICENSE=|| ( Artistic GPL-1+ ) -RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:= -RESTRICT=test -SLOT=0 -SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz -_eclasses_=multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 -_md5_=dbcb977782edcacd68dddedab8e605d9 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 deleted file mode 100644 index 4972ff9cddd5..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] dev-vcs/git -DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -LICENSE=Artistic GPL-2 -RDEPEND=>=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] -SLOT=0 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=fd4229be06b3975302e9e37ca35601d2 diff --git a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 deleted file mode 100644 index bbca2bd83e36..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] -DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=test -KEYWORDS=amd64 x86 -LICENSE=|| ( Artistic GPL-1+ ) -RDEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] -SLOT=0 -SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Network-1.006900.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=cb366a6a0c6cf3c12320c2d6d3551abe diff --git a/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 deleted file mode 100644 index 8c77204ad407..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] dev-vcs/git -DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=test -LICENSE=Artistic GPL-2 -RDEPEND=>=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] -SLOT=0 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=025cd5fa89be402f3296160dbf755c8b diff --git a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 deleted file mode 100644 index 82aecc5602b4..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] -DESCRIPTION=Perl wrapper modules for key bioinformatics applications -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=-minimal test -KEYWORDS=amd64 x86 -LICENSE=|| ( Artistic GPL-1+ ) -RDEPEND=>=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] -RESTRICT=test -SLOT=0 -SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=9caec4e5b47cbf306a1689903f2a018a diff --git a/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 deleted file mode 100644 index d129942579c7..000000000000 --- a/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] dev-vcs/git -DESCRIPTION=Perl wrapper modules for key bioinformatics applications -EAPI=5 -HOMEPAGE=http://www.bioperl.org/ -IUSE=-minimal test -LICENSE=Artistic GPL-2 -RDEPEND=>=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] -RESTRICT=test -SLOT=0 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=26abe4f8477c1a1c22bd8515484ce1c1 diff --git a/metadata/md5-cache/sci-biology/biopython-1.68 b/metadata/md5-cache/sci-biology/biopython-1.68 deleted file mode 100644 index 43966c7c4c84..000000000000 --- a/metadata/md5-cache/sci-biology/biopython-1.68 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install postinst prepare test -DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] sys-devel/flex python_targets_pypy? ( >=virtual/pypy-5:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] -DESCRIPTION=Python modules for computational molecular biology -EAPI=6 -HOMEPAGE=http://www.biopython.org/ https://pypi.org/project/biopython/ -IUSE=python_targets_pypy python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=HPND -RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] python_targets_pypy? ( >=virtual/pypy-5:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] -REQUIRED_USE=|| ( python_targets_pypy python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 ) -SLOT=0 -SRC_URI=http://www.biopython.org/DIST/biopython-1.68.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=d27e2e9df832a55985e7f459f9e4fa81 diff --git a/metadata/md5-cache/sci-biology/biopython-1.71 b/metadata/md5-cache/sci-biology/biopython-1.71 deleted file mode 100644 index d18ebe157bfb..000000000000 --- a/metadata/md5-cache/sci-biology/biopython-1.71 +++ /dev/null @@ -1,15 +0,0 @@ -BDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -DEFINED_PHASES=compile configure install postinst prepare test -DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/networkx[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/rdflib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/reportlab[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pydot[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sys-devel/flex -DESCRIPTION=Python modules for computational molecular biology -EAPI=7 -HOMEPAGE=https://www.biopython.org/ https://pypi.org/project/biopython/ -IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=HPND -RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/networkx[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/rdflib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/reportlab[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pydot[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) -SLOT=0 -SRC_URI=mirror://pypi/b/biopython/biopython-1.71.tar.gz -_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 eutils 5b8ce72259e08104b337fe28c6de5dbc multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=0227795578e2ffd9791cbebddc3ee0ab diff --git a/metadata/md5-cache/sci-biology/bioruby-1.5.1 b/metadata/md5-cache/sci-biology/bioruby-1.5.1 deleted file mode 100644 index 46286a345e55..000000000000 --- a/metadata/md5-cache/sci-biology/bioruby-1.5.1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test unpack -DEPEND=test? ( ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby23? ( doc? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby24? ( doc? ( dev-ruby/rake[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( test? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby24? ( test? ( dev-ruby/rake[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) test? ( ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) ) -DESCRIPTION=An integrated environment for bioinformatics using the Ruby language -EAPI=6 -HOMEPAGE=http://bioruby.org/ -IUSE=test elibc_FreeBSD ruby_targets_ruby23 ruby_targets_ruby24 doc test test -KEYWORDS=amd64 ~ppc x86 -LICENSE=Ruby -RDEPEND=ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24] ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) -REQUIRED_USE=|| ( ruby_targets_ruby23 ruby_targets_ruby24 ) -SLOT=0 -SRC_URI=mirror://rubygems/bio-1.5.1.gem -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 ruby-fakegem 28631ba8ae1b3218596c0eb3e38c438e ruby-ng c1f44e746d7656dd6e02d8815ff9518a ruby-utils e5942a80e3c3b936c6b84d6dc4af9f9c toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=2aecf9a558ab9d1f3e8760530ccd8e56 diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 deleted file mode 100644 index 2a7fa17d9aa9..000000000000 --- a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=install postinst -DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) -DESCRIPTION=A generic bioinformatics relational database model -EAPI=6 -HOMEPAGE=http://www.biosql.org/ -IUSE=mysql postgres -KEYWORDS=amd64 x86 -LICENSE=LGPL-3 -RDEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) dev-lang/perl -SLOT=0 -SRC_URI=http://biosql.org/DIST/biosql-1.0.1.tar.bz2 -_md5_=c3363146ed9daed7fd12e748db91abe0 diff --git a/metadata/md5-cache/sci-biology/blat-34-r2 b/metadata/md5-cache/sci-biology/blat-34-r2 deleted file mode 100644 index c30336f803de..000000000000 --- a/metadata/md5-cache/sci-biology/blat-34-r2 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=app-arch/unzip -DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner -EAPI=6 -HOMEPAGE=http://www.cse.ucsc.edu/~kent/ -KEYWORDS=~amd64 ~x86 -LICENSE=blat -SLOT=0 -SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=d48361335699038107318f5ca57533e8 diff --git a/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 b/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 deleted file mode 100644 index 877066c25789..000000000000 --- a/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=sci-libs/gsl:= dev-libs/boost:= sci-biology/snpfile >=sys-devel/autoconf-archive-2016.09.16 virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A linkage disequilibrium association mapping tool -EAPI=6 -HOMEPAGE=http://www.daimi.au.dk/~mailund/Blossoc/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=sci-libs/gsl:= dev-libs/boost:= sci-biology/snpfile -SLOT=0 -SRC_URI=http://www.daimi.au.dk/~mailund/Blossoc/download/blossoc-1.4.0.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=2fe1853c7621b633d2ee794ef3176e3f diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 deleted file mode 100644 index e07e0261fe74..000000000000 --- a/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=tbb? ( dev-cpp/tbb ) sci-biology/seqan:1.4 app-arch/unzip -DESCRIPTION=Popular short read aligner for Next-generation sequencing data -EAPI=6 -HOMEPAGE=http://bowtie-bio.sourceforge.net/ -IUSE=examples +tbb -KEYWORDS=~amd64 ~x86 ~x64-macos -LICENSE=Artistic -RDEPEND=tbb? ( dev-cpp/tbb ) -SLOT=1 -SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=069dc133bc01cabadeda1e327034b7a7 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.9 b/metadata/md5-cache/sci-biology/bowtie-2.2.9 deleted file mode 100644 index f3b30dad12b3..000000000000 --- a/metadata/md5-cache/sci-biology/bowtie-2.2.9 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install pretend -DEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) app-arch/unzip -DESCRIPTION=Popular short read aligner for Next-generation sequencing data -EAPI=6 -HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ -IUSE=examples cpu_flags_x86_sse2 +tbb -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) -SLOT=2 -SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-source.zip -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=46d87c867cd445707dc1913cf3dd7eb6 diff --git a/metadata/md5-cache/sci-biology/bwa-0.7.16a b/metadata/md5-cache/sci-biology/bwa-0.7.16a deleted file mode 100644 index 782a1481c347..000000000000 --- a/metadata/md5-cache/sci-biology/bwa-0.7.16a +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner -EAPI=6 -HOMEPAGE=https://bio-bwa.sourceforge.net/ -KEYWORDS=~amd64 ~x86 ~x64-macos -LICENSE=GPL-3 -RDEPEND=dev-lang/perl -SLOT=0 -SRC_URI=mirror://sourceforge/bio-bwa/bwa-0.7.16a.tar.bz2 -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=b3702a6accf64398e32e84076031919b diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 deleted file mode 100644 index 6779bec7281c..000000000000 --- a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install pretend setup -DESCRIPTION=Clustering Database at High Identity with Tolerance -EAPI=6 -HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ -IUSE=openmp -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=GPL-2 -RDEPEND=dev-lang/perl -SLOT=0 -SRC_URI=https://github.com/weizhongli/cdhit/releases/download/V4.6.6/cd-hit-v4.6.6-2016-0711.tar.gz -> cd-hit-4.6.6.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=bbe0ae10275a73485487e08f19f4ac1b diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 deleted file mode 100644 index 1cdae250f16a..000000000000 --- a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=dev-libs/argtable >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Scalable multiple alignment of protein sequences -EAPI=6 -HOMEPAGE=http://www.clustal.org/omega/ -IUSE=static-libs -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=dev-libs/argtable -SLOT=0 -SRC_URI=http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=9ade45d2e283bc5fcc7eef16725e18ae diff --git a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 deleted file mode 100644 index d8853bcdbf96..000000000000 --- a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=General purpose multiple alignment program for DNA and proteins -EAPI=6 -HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ -KEYWORDS=alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=clustalw -SLOT=1 -SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=5c8ba46cd87128b1ddae72e6ca3d07db diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 deleted file mode 100644 index 5e8138428bfc..000000000000 --- a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 +++ /dev/null @@ -1,9 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=General purpose multiple alignment program for DNA and proteins -EAPI=6 -HOMEPAGE=http://www.clustal.org/ -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=GPL-3 LGPL-3 -SLOT=2 -SRC_URI=http://www.clustal.org/download/current/clustalw-2.1.tar.gz -_md5_=397de2c00339f3a0b847f6daa9a481fb diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 deleted file mode 100644 index c38b18613df1..000000000000 --- a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=virtual/mpi -DESCRIPTION=An MPI implemention of the ClustalW general purpose multiple alignment algorithm -EAPI=6 -HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php -IUSE=mpi_njtree static_pairalign -KEYWORDS=~amd64 ~x86 -LICENSE=public-domain -RDEPEND=virtual/mpi -SLOT=0 -SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=9e376a1d2ae782d9495b0c6c318aa097 diff --git a/metadata/md5-cache/sci-biology/clustalx-2.1-r3 b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 deleted file mode 100644 index 0c6f45783eef..000000000000 --- a/metadata/md5-cache/sci-biology/clustalx-2.1-r3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 -DESCRIPTION=Graphical interface for the ClustalW multiple alignment program -EAPI=6 -HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/ -KEYWORDS=amd64 x86 -LICENSE=GPL-3 LGPL-3 -RDEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 >=sci-biology/clustalw-2.1 -SLOT=0 -SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz https://dev.gentoo.org/~jlec/distfiles/clustalx.png.xz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 estack 43ddf5aaffa7a8d0482df54d25a66a1f multilib 97f470f374f2e94ccab04a2fb21d811e qmake-utils bdf97e69a34b864d6d545f4ec3143ff7 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=c8dbd602c40010526edb4955aa67e1b3 diff --git a/metadata/md5-cache/sci-biology/consed-29 b/metadata/md5-cache/sci-biology/consed-29 deleted file mode 100644 index 274f6f028c74..000000000000 --- a/metadata/md5-cache/sci-biology/consed-29 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install nofetch postinst prepare -DEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy virtual/pkgconfig -DESCRIPTION=A genome sequence finishing program -EAPI=6 -HOMEPAGE=http://bozeman.mbt.washington.edu/consed/consed.html -IUSE=examples -KEYWORDS=~amd64 ~x86 -LICENSE=phrap -RDEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy dev-lang/perl >=sci-biology/phred-071220-r1 >=sci-biology/phrap-1.080812-r2 -RESTRICT=fetch -SLOT=0 -SRC_URI=consed-29-sources.tar.gz consed-29-linux.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=d533d3bc63ad3989cce879478db9de97 diff --git a/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 b/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 deleted file mode 100644 index 3502a8fe306b..000000000000 --- a/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure prepare setup -DEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.62.0:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-cpp/eigen:3 virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Transcript assembly and differential expression/regulation for RNA-Seq -EAPI=6 -HOMEPAGE=http://cufflinks.cbcb.umd.edu/ -IUSE=debug python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.62.0:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=8e0065b0f455fa63e987f6182ed61fa1 diff --git a/metadata/md5-cache/sci-biology/cutg-160-r1 b/metadata/md5-cache/sci-biology/cutg-160-r1 deleted file mode 100644 index 60c35396bc6a..000000000000 --- a/metadata/md5-cache/sci-biology/cutg-160-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( sci-biology/emboss ) -DESCRIPTION=Codon usage tables calculated from GenBank -EAPI=5 -HOMEPAGE=http://www.kazusa.or.jp/codon/ -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=emboss? ( sci-biology/emboss ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/cutg-160.tar.xz -_md5_=bbbd347ac6eafe2416778cd68a45bf1a diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 deleted file mode 100644 index a36dedd8ac96..000000000000 --- a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile configure install postinst -DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment -EAPI=6 -HOMEPAGE=http://dialign-tx.gobics.de/ -KEYWORDS=~amd64 ~x86 -LICENSE=LGPL-2.1 -SLOT=0 -SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=b04d9beffea802bb82f896df101ca660 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1 deleted file mode 100644 index 9c9985528a11..000000000000 --- a/metadata/md5-cache/sci-biology/dialign2-2.2.1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile configure install -DESCRIPTION=Multiple sequence alignment -EAPI=6 -HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2.1 -SLOT=0 -SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=3761a69a47f38308f54ae0b051361ed6 diff --git a/metadata/md5-cache/sci-biology/diya-1.0_rc4 b/metadata/md5-cache/sci-biology/diya-1.0_rc4 deleted file mode 100644 index d643878f6527..000000000000 --- a/metadata/md5-cache/sci-biology/diya-1.0_rc4 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple dev-lang/perl:=[-build(-)] -DESCRIPTION=Do It Yourself Annotation, tools & libraries for sequence assembly & annotation -EAPI=5 -HOMEPAGE=http://gmod.org/wiki/Diya -IUSE=-minimal -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple !minimal? ( sci-biology/mummer sci-biology/glimmer sci-biology/trnascan-se sci-biology/infernal ) dev-lang/perl:=[-build(-)] -SLOT=0 -SRC_URI=mirror://sourceforge/diyg/files/diya/diya-1.0/diya-1.0-rc4.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=5d4639d7c08c43e2c2208492508fd56c diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 deleted file mode 100644 index ce03af7423a3..000000000000 --- a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program -EAPI=6 -HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=Artistic -SLOT=0 -SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=dbee2f511488caf9eadadb20d043a2da diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 deleted file mode 100644 index d501a327e417..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 +++ /dev/null @@ -1,9 +0,0 @@ -DEFINED_PHASES=- -DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/embassy/ -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=freedist -RDEPEND=>=sci-biology/embassy-cbstools-1.0.0.660 >=sci-biology/embassy-clustalomega-1.1.0.660 >=sci-biology/embassy-domainatrix-0.1.660 >=sci-biology/embassy-domalign-0.1.660 >=sci-biology/embassy-domsearch-0.1.660 >=sci-biology/embassy-emnu-1.05.660 >=sci-biology/embassy-esim4-1.0.0.660 >=sci-biology/embassy-hmmer-2.3.2.660 >=sci-biology/embassy-iprscan-4.3.1.660 >=sci-biology/embassy-meme-4.7.660 >=sci-biology/embassy-mse-3.0.0.660 >=sci-biology/embassy-phylipnew-3.69.660 >=sci-biology/embassy-signature-0.1.660 >=sci-biology/embassy-structure-0.1.660 >=sci-biology/embassy-topo-2.0.660 >=sci-biology/embassy-vienna-1.7.2.660 -SLOT=0 -_md5_=40fa8435e29624ec5b0c9ffaf2b8c695 diff --git a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 deleted file mode 100644 index baccb8015dcb..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Applications from the CBS group -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.660.tar.gz -> embassy-cbstools-1.0.0.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=4166ba28131fdf70907b31300aa4c08b diff --git a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 deleted file mode 100644 index fb44e625c855..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=sci-biology/clustal-omega dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-1.1.0.660.tar.gz -> embassy-clustalomega-1.1.0.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=ef491b452e56be12961f62b16961f4f1 diff --git a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 deleted file mode 100644 index d90c639fdc35..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Protein domain analysis add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.660.tar.gz -> embassy-domainatrix-0.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=bfee4f5b2b2adadb41de2eb02d4dcbc0 diff --git a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 deleted file mode 100644 index 9e40b3a871ac..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Protein domain alignment add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.660.tar.gz -> embassy-domalign-0.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=9f8b2caa273f4ae3b0463e6de6782660 diff --git a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 deleted file mode 100644 index d35d5fdbbd8f..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Protein domain search add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.660.tar.gz -> embassy-domsearch-0.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=920906439fbc5278460201b23a615736 diff --git a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 deleted file mode 100644 index a52347cebf80..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=ncurses mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.660.tar.gz -> embassy-emnu-1.05.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=d82c7c44ec76fa5d6165769a73e5df9a diff --git a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 deleted file mode 100644 index 4c156e4ede39..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.660.tar.gz -> embassy-esim4-1.0.0.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=1b156bed7ea031aeb5464836dd987f18 diff --git a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 deleted file mode 100644 index 3a606d66366e..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=sci-biology/hmmer:2 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.660.tar.gz -> embassy-hmmer-2.3.2.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=83d02ae22d4e1864669639d9289cd112 diff --git a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 deleted file mode 100644 index 21516fe8e442..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of InterProScan motif detection add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.660.tar.gz -> embassy-iprscan-4.3.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=73b0c29964ea3506d18ef6b6c8df70e1 diff --git a/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 b/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 deleted file mode 100644 index aeedd6b9ef2e..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=sci-biology/meme dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.660.tar.gz -> embassy-meme-4.7.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=b18db6d7a2159272c7b69d34a14dc9b5 diff --git a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 deleted file mode 100644 index ab994f1cc0d7..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of MSE - Multiple Sequence Screen Editor -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=ncurses mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.660.tar.gz -> embassy-mse-3.0.0.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=84df94b7c4b0f044de45cef524cbf453 diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 deleted file mode 100644 index adc1702b4f1f..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of The Phylogeny Inference Package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 freedist -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.660.tar.gz -> embassy-phylipnew-3.69.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=00620d36fbf4790dc2ecfb240ba9816c diff --git a/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 deleted file mode 100644 index 31cabf1ff6a0..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Protein signature add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.660.tar.gz -> embassy-signature-0.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=4cb685046b5a39b624eb3467b815c2c4 diff --git a/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 deleted file mode 100644 index 768f5143a4e2..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Protein structure add-on package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.660.tar.gz -> embassy-structure-0.1.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=634d624be78f958ed7fca02e7dc43bd4 diff --git a/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 b/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 deleted file mode 100644 index 7ebd1bf01815..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Transmembrane protein display -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.660.tar.gz -> embassy-topo-2.0.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=e50220ee11093554b589c1f9f53e7c09 diff --git a/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 deleted file mode 100644 index 48e5f998a81d..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -DESCRIPTION=EMBOSS integrated version of Vienna RNA package - RNA folding -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 -RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.660.tar.gz -> embassy-vienna-1.7.2.660.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=d257de40bcdb33c0735daac8a5f15fda diff --git a/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 b/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 deleted file mode 100644 index 0367e764d745..000000000000 --- a/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install postinst prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) -DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package -EAPI=6 -HOMEPAGE=http://emboss.sourceforge.net/ -IUSE=minimal mysql pdf png postgres static-libs X -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 -PDEPEND=!minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase ) -RDEPEND=!games-action/xbomber !sys-devel/cons dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) -SLOT=0 -SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 readme.gentoo-r1 54aecea034d5e90bdb0684b80da5c9f3 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=99a47266a2a8f2fd0a874111491146e2 diff --git a/metadata/md5-cache/sci-biology/eugene-4.1d b/metadata/md5-cache/sci-biology/eugene-4.1d deleted file mode 100644 index a64950a48fbd..000000000000 --- a/metadata/md5-cache/sci-biology/eugene-4.1d +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=media-libs/gd[png] media-libs/libpng:0= >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Prokaryotic and Eukaryotic gene predictor -EAPI=6 -HOMEPAGE=http://eugene.toulouse.inra.fr/ -KEYWORDS=amd64 x86 -LICENSE=Artistic -RDEPEND=media-libs/gd[png] media-libs/libpng:0= -RESTRICT=test -SLOT=0 -SRC_URI=https://mulcyber.toulouse.inra.fr/frs/download.php/1359/eugene-4.1d.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=683d1e7f9daeda6cd20b92117330ea81 diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 deleted file mode 100644 index 4cf4d02e74b4..000000000000 --- a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=dev-libs/glib:2 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Generic tool for pairwise sequence comparison -EAPI=6 -HOMEPAGE=https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate -IUSE=test threads utils -KEYWORDS=~amd64 ~x86 ~ppc-macos ~x64-macos -LICENSE=GPL-3 -RDEPEND=dev-libs/glib:2 -REQUIRED_USE=test? ( utils ) -SLOT=0 -SRC_URI=http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=2efd53d13e6f08e4144477038f41e4af diff --git a/metadata/md5-cache/sci-biology/express-0.9.5-r1 b/metadata/md5-cache/sci-biology/express-0.9.5-r1 deleted file mode 100644 index c1d1a38cd561..000000000000 --- a/metadata/md5-cache/sci-biology/express-0.9.5-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=dev-libs/boost-1.52.0:= sys-libs/zlib sci-biology/bamtools sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=Streaming RNA-Seq Analysis -EAPI=5 -HOMEPAGE=http://bio.math.berkeley.edu/eXpress/ -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=>=dev-libs/boost-1.52.0:= sys-libs/zlib sci-biology/bamtools -SLOT=0 -SRC_URI=http://bio.math.berkeley.edu/eXpress/downloads/express-0.9.5/express-0.9.5-src.tgz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=6d15a446bfc7659cceaabe3567001583 diff --git a/metadata/md5-cache/sci-biology/express-1.5.1 b/metadata/md5-cache/sci-biology/express-1.5.1 deleted file mode 100644 index 1e7c4ce21732..000000000000 --- a/metadata/md5-cache/sci-biology/express-1.5.1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=dev-libs/boost-1.52.0:= dev-libs/protobuf dev-util/google-perftools sys-libs/zlib sci-biology/bamtools sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=Streaming RNA-Seq Analysis -EAPI=5 -HOMEPAGE=http://bio.math.berkeley.edu/eXpress/ -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=>=dev-libs/boost-1.52.0:= dev-libs/protobuf dev-util/google-perftools sys-libs/zlib sci-biology/bamtools -SLOT=0 -SRC_URI=http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=a2d4ea80b964801c45f62ae737430d6d diff --git a/metadata/md5-cache/sci-biology/fasta-36.3.5e b/metadata/md5-cache/sci-biology/fasta-36.3.5e deleted file mode 100644 index c196af799578..000000000000 --- a/metadata/md5-cache/sci-biology/fasta-36.3.5e +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare test -DEPEND=test? 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( double-precision cpu_flags_x86_sse3 ) -SLOT=0 -SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.8.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.8.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.8.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=f2b648d93a4c0ca58285574958cde15a diff --git a/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14 b/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14 deleted file mode 100644 index 60b0ecbed51e..000000000000 --- a/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=sci-biology/libgtextutils virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Tools for Short Read FASTA/FASTQ file processing -EAPI=6 -HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit -KEYWORDS=~amd64 ~x86 -LICENSE=AGPL-3 -RDEPEND=dev-perl/PerlIO-gzip dev-perl/GDGraph sci-biology/libgtextutils:= sci-visualization/gnuplot -SLOT=0 -SRC_URI=https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=c3bb0edd6b01a31019cf5fd59e22122a diff --git a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 deleted file mode 100644 index dd4a6f663f72..000000000000 --- a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2 +++ /dev/null @@ -1,9 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=Graphical viewer for chromatogram files -EAPI=5 -HOMEPAGE=http://www.geospiza.com/finchtv/ -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=finchtv -SLOT=0 -SRC_URI=http://www.geospiza.com/finchtv/download/programs/linux/finchtv_1_3_1.tar.gz -_md5_=ae49772a5dce24695f0ae65993bae0c1 diff --git a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3 b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3 deleted file mode 100644 index f32ba8cb0d34..000000000000 --- a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=Graphical viewer for chromatogram files -EAPI=6 -HOMEPAGE=http://www.geospiza.com/finchtv/ -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=finchtv -SLOT=0 -SRC_URI=http://www.geospiza.com/finchtv/download/programs/linux/finchtv_1_3_1.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=08355830f28d1052c2ab527b82a8dd68 diff --git a/metadata/md5-cache/sci-biology/foldingathome-7.4.4-r3 b/metadata/md5-cache/sci-biology/foldingathome-7.4.4-r3 deleted file mode 100644 index de0cf5cb22ab..000000000000 --- a/metadata/md5-cache/sci-biology/foldingathome-7.4.4-r3 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=config install postinst postrm setup -DEPEND=virtual/pkgconfig -DESCRIPTION=Folding@Home is a distributed computing project for protein folding -EAPI=6 -HOMEPAGE=http://folding.stanford.edu/FAQ-SMP.html -KEYWORDS=~amd64 ~x86 -LICENSE=FAH-EULA-2014 FAH-special-permission -RDEPEND=app-arch/bzip2 sys-devel/gcc sys-libs/glibc sys-libs/zlib -RESTRICT=mirror bindist strip -SLOT=0 -SRC_URI=x86? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.5-32bit/v7.4/fahclient_7.4.4-32bit-release.tar.bz2 ) amd64? 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( virtual/mpi sys-cluster/mpe2 ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Identify motifs, conserved regions, in DNA or protein sequences -EAPI=4 -HOMEPAGE=http://bayesweb.wadsworth.org/gibbs/gibbs.html -IUSE=mpi -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) -SLOT=0 -SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=e28918ff8ca46c8b8254e4e36f8d0bcf diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 deleted file mode 100644 index 541d3d024994..000000000000 --- a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=An HMM-based microbial gene finding system from TIGR -EAPI=5 -HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml -KEYWORDS=amd64 x86 -LICENSE=Artistic -RDEPEND=app-shells/tcsh -SLOT=0 -SRC_URI=http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=94600a4de5a2dc02bc6652d958a2a034 diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02b b/metadata/md5-cache/sci-biology/glimmer-3.02b deleted file mode 100644 index a54e581a23ed..000000000000 --- a/metadata/md5-cache/sci-biology/glimmer-3.02b +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=An HMM-based microbial gene finding system from TIGR -EAPI=5 -HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=app-shells/tcsh sci-biology/elph -SLOT=0 -SRC_URI=https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=6916d92c69198563f19b744f1e57dddc diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 deleted file mode 100644 index c532987d4635..000000000000 --- a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile install prepare unpack -DESCRIPTION=A eukaryotic gene finding system from TIGR -EAPI=4 -HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ -KEYWORDS=amd64 x86 -LICENSE=Artistic -SLOT=0 -SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=addae30e588a0c7a05baea53d553af0f diff --git a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 deleted file mode 100644 index 735b548494bd..000000000000 --- a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=- -DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences -EAPI=6 -HOMEPAGE=http://research-pub.gene.com/gmap/ -KEYWORDS=~amd64 ~x86 -LICENSE=gmap -SLOT=0 -SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-12-31.v5.tar.gz -_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=398e7f0670f5bd07e45f2780d7fe03cf diff --git a/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 b/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 deleted file mode 100644 index 242a42be0c46..000000000000 --- a/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install preinst prepare setup -DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 -DESCRIPTION=A DNA sequencing data 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( ~sci-biology/goby-cpp-1.9.7.3 ) >=dev-java/java-config-2.2.0-r3 -SLOT=0 -SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-deps.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=d8bbf59f45f0b32b55de88f3c5233883 diff --git a/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 b/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 deleted file mode 100644 index 9a6f81f6f1c7..000000000000 --- a/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install preinst prepare setup -DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 -DESCRIPTION=A DNA sequencing data management framework -EAPI=4 -HOMEPAGE=http://campagnelab.org/software/goby/ -IUSE=+cpp elibc_FreeBSD elibc_FreeBSD -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 LGPL-3 -RDEPEND=>=virtual/jre-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 cpp? ( ~sci-biology/goby-cpp-1.9.8.1 ) >=dev-java/java-config-2.2.0-r3 -SLOT=0 -SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-deps.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=d8bbf59f45f0b32b55de88f3c5233883 diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 deleted file mode 100644 index 3ac995e65ff6..000000000000 --- a/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A DNA sequencing data management framework - C/C++ API -EAPI=4 -HOMEPAGE=http://campagnelab.org/software/goby/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 -SLOT=0 -SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-cpp.zip -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=62b1fc794a90a87e0f80ab795108ee3c diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 deleted file mode 100644 index d149666d18af..000000000000 --- a/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A DNA sequencing data management framework - C/C++ API -EAPI=4 -HOMEPAGE=http://campagnelab.org/software/goby/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 -SLOT=0 -SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-cpp.zip -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=2599766d541e65f4acfb94c4fa4e974e diff --git a/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 b/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 deleted file mode 100644 index 96facd392962..000000000000 --- a/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A DNA sequencing data management framework - C/C++ API -EAPI=5 -HOMEPAGE=http://campagnelab.org/software/goby/ -IUSE=static-libs -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 -SLOT=0 -SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_2.0.1/goby_2.0.1-cpp.zip https://dev.gentoo.org/~mgorny/dist/goby-cpp-2.0.1-files.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=8282c100b202c470aedc98e37f6151ff diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 deleted file mode 100644 index 58b40abe2b1b..000000000000 --- a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install postinst -DEPEND=test? ( dev-lang/perl ) -DESCRIPTION=Sequence analysis using profile hidden Markov models -EAPI=6 -HOMEPAGE=http://hmmer.org/ -IUSE=altivec test threads -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=2 -SRC_URI=http://eddylab.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz -_md5_=2f631b79914f25875fd00c05fd144807 diff --git a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 deleted file mode 100644 index c098b0527d7b..000000000000 --- a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure install -DEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) test? ( dev-lang/perl ) -DESCRIPTION=Sequence analysis using profile hidden Markov models -EAPI=6 -HOMEPAGE=http://hmmer.org/ -IUSE=altivec cpu_flags_x86_sse gsl mpi test +threads -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=GPL-3 -RDEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) -SLOT=0 -SRC_URI=http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz -_md5_=e1fda24a135e4e71cdf6ae399f38faea diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r1 b/metadata/md5-cache/sci-biology/iedera-1.05-r1 deleted file mode 100644 index 38c179af61ab..000000000000 --- a/metadata/md5-cache/sci-biology/iedera-1.05-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A subset seed design tool for DNA sequence alignment -EAPI=6 -HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=ce77e1e27bd52fed2fd2af52744d6288 diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 deleted file mode 100644 index e3d478338308..000000000000 --- a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure install -DEPEND=mpi? ( virtual/mpi ) -DESCRIPTION=Inference of RNA alignments -EAPI=6 -HOMEPAGE=http://infernal.janelia.org/ -IUSE=mpi -KEYWORDS=amd64 x86 -LICENSE=GPL-3 -RDEPEND=mpi? ( virtual/mpi ) -SLOT=0 -SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz -_md5_=a3cee86cfd4ecbef4e39563bc652a64b diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 deleted file mode 100644 index 975248a39250..000000000000 --- a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=Important Quartet Puzzling and NNI Operation -EAPI=6 -HOMEPAGE=http://www.cibiv.at/software/iqpnni/ -IUSE=doc -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.3.2.tar.gz -_md5_=871193b79341fc00590227fc8ec7d4d4 diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r2 b/metadata/md5-cache/sci-biology/kalign-2.03-r2 deleted file mode 100644 index 57f478bea557..000000000000 --- a/metadata/md5-cache/sci-biology/kalign-2.03-r2 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Global and progressive multiple sequence alignment -EAPI=6 -HOMEPAGE=http://msa.cgb.ki.se/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=175d26382226c7bed2b44be485b01d01 diff --git a/metadata/md5-cache/sci-biology/kallisto-0.43.1 b/metadata/md5-cache/sci-biology/kallisto-0.43.1 deleted file mode 100644 index 6de6239d5694..000000000000 --- a/metadata/md5-cache/sci-biology/kallisto-0.43.1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=sci-libs/hdf5:= sys-libs/zlib:= sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=Near-optimal RNA-Seq quantification -EAPI=6 -HOMEPAGE=http://pachterlab.github.io/kallisto/ -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=BSD -RDEPEND=sci-libs/hdf5:= sys-libs/zlib:= -SLOT=0 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a/metadata/md5-cache/sci-biology/kallisto-9999 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=sci-libs/hdf5:= sys-libs/zlib:= sys-devel/make >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] -DESCRIPTION=Near-optimal RNA-Seq quantification -EAPI=6 -HOMEPAGE=http://pachterlab.github.io/kallisto/ -LICENSE=BSD -RDEPEND=sci-libs/hdf5:= sys-libs/zlib:= -SLOT=0 -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=b5fc562bf49e70db44b86bc5702ae9f2 diff --git a/metadata/md5-cache/sci-biology/lagan-2.0-r3 b/metadata/md5-cache/sci-biology/lagan-2.0-r3 deleted file mode 100644 index 8ab697e07162..000000000000 --- a/metadata/md5-cache/sci-biology/lagan-2.0-r3 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA -EAPI=6 -HOMEPAGE=http://lagan.stanford.edu/lagan_web/index.shtml -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=dev-lang/perl -SLOT=0 -SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=c9dbddd6a22f2e20ff25d0aa1e6f4280 diff --git a/metadata/md5-cache/sci-biology/last-230 b/metadata/md5-cache/sci-biology/last-230 deleted file mode 100644 index a255bb1fc8fb..000000000000 --- a/metadata/md5-cache/sci-biology/last-230 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=app-arch/unzip -DESCRIPTION=Genome-scale comparison of biological sequences -EAPI=4 -HOMEPAGE=http://last.cbrc.jp/ -KEYWORDS=amd64 x86 -LICENSE=GPL-3 -SLOT=0 -SRC_URI=http://last.cbrc.jp/archive/last-230.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=5da658e6779591b0d1b9ad3413a0e7b2 diff --git a/metadata/md5-cache/sci-biology/last-299-r1 b/metadata/md5-cache/sci-biology/last-299-r1 deleted file mode 100644 index e65d8edd8a73..000000000000 --- a/metadata/md5-cache/sci-biology/last-299-r1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install setup -DEPEND=app-arch/unzip -DESCRIPTION=Genome-scale comparison of biological sequences -EAPI=6 -HOMEPAGE=http://last.cbrc.jp/ -IUSE=python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=http://last.cbrc.jp/last-299.zip -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=ec5206661373a6ef6ad77450dfbdb915 diff --git a/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 deleted file mode 100644 index 198af655822a..000000000000 --- a/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Gordon Text utils Library -EAPI=6 -HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit/ -KEYWORDS=~amd64 ~x86 -LICENSE=AGPL-3 -SLOT=0/0 -SRC_URI=http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.1.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=867c9b9e4eee26ad2a76ff6ff0594f52 diff --git a/metadata/md5-cache/sci-biology/mafft-7.050 b/metadata/md5-cache/sci-biology/mafft-7.050 deleted file mode 100644 index 7b4bc2396e82..000000000000 --- a/metadata/md5-cache/sci-biology/mafft-7.050 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare test -DESCRIPTION=Multiple sequence alignments using a variety of algorithms -EAPI=5 -HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html -IUSE=threads -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos -LICENSE=BSD -SLOT=0 -SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.050-without-extensions-src.tgz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=3195e77c5c792018208b65f5dbeab567 diff --git a/metadata/md5-cache/sci-biology/mafft-7.215 b/metadata/md5-cache/sci-biology/mafft-7.215 deleted file mode 100644 index 960656eb2384..000000000000 --- a/metadata/md5-cache/sci-biology/mafft-7.215 +++ /dev/null @@ -1,11 +0,0 @@ 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a/metadata/md5-cache/sci-biology/maq-0.7.1-r2 b/metadata/md5-cache/sci-biology/maq-0.7.1-r2 deleted file mode 100644 index cc8309cd4378..000000000000 --- a/metadata/md5-cache/sci-biology/maq-0.7.1-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sys-libs/zlib >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes -EAPI=6 -HOMEPAGE=http://maq.sourceforge.net/ -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=GPL-3 -RDEPEND=sys-libs/zlib -SLOT=0 -SRC_URI=mirror://sourceforge/maq/maq-0.7.1.tar.bz2 mirror://sourceforge/maq/calib-36.dat.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=39ffb0025210075a8d7d7f6f81f8da56 diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 deleted file mode 100644 index 407b0049f7f1..000000000000 --- a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=media-libs/freeglut sys-libs/zlib >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler -EAPI=6 -HOMEPAGE=http://maq.sourceforge.net/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=media-libs/freeglut sys-libs/zlib sci-biology/maq -SLOT=0 -SRC_URI=mirror://sourceforge/maq/maqview-0.2.5.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=dee50558d10e75ff9e96f4c3f177c55f diff --git a/metadata/md5-cache/sci-biology/mcl-08.312 b/metadata/md5-cache/sci-biology/mcl-08.312 deleted file mode 100644 index a0c07208af25..000000000000 --- a/metadata/md5-cache/sci-biology/mcl-08.312 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A Markov Cluster Algorithm implementation -EAPI=4 -HOMEPAGE=http://micans.org/mcl/ -IUSE=+blast -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://micans.org/mcl/src/mcl-08-312.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=24cf3aad7375304f2721048d2f76b5f1 diff --git a/metadata/md5-cache/sci-biology/mcl-12.135 b/metadata/md5-cache/sci-biology/mcl-12.135 deleted file mode 100644 index e4d6b16efd80..000000000000 --- a/metadata/md5-cache/sci-biology/mcl-12.135 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A Markov Cluster Algorithm implementation -EAPI=4 -HOMEPAGE=http://micans.org/mcl/ -IUSE=+blast -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://micans.org/mcl/src/mcl-12-135.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=24cf3aad7375304f2721048d2f76b5f1 diff --git a/metadata/md5-cache/sci-biology/mcl-14.137 b/metadata/md5-cache/sci-biology/mcl-14.137 deleted file mode 100644 index c01e319373af..000000000000 --- a/metadata/md5-cache/sci-biology/mcl-14.137 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A Markov Cluster Algorithm implementation -EAPI=6 -HOMEPAGE=http://micans.org/mcl/ -IUSE=+blast -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://micans.org/mcl/src/mcl-14-137.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=3429c68609b6c70e047d577379f68f97 diff --git a/metadata/md5-cache/sci-biology/meme-4.11.2_p2 b/metadata/md5-cache/sci-biology/meme-4.11.2_p2 deleted file mode 100644 index 078207f58052..000000000000 --- a/metadata/md5-cache/sci-biology/meme-4.11.2_p2 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install prepare setup test -DEPEND=python_targets_python2_7? 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( virtual/mpi ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=The MEME/MAST system - Motif discovery and search -EAPI=6 -HOMEPAGE=http://meme-suite.org/tools/meme -IUSE=debug doc examples mpi python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=meme -RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] app-shells/tcsh dev-libs/libxml2:2 dev-libs/libxslt sys-libs/zlib app-text/ghostscript-gpl media-gfx/imagemagick dev-lang/perl:= dev-perl/HTML-Parser dev-perl/HTML-Template dev-perl/Log-Log4perl dev-perl/Math-CDF dev-perl/XML-Compile-SOAP dev-perl/XML-Compile-WSDL11 dev-perl/XML-Parser dev-perl/XML-Simple virtual/perl-Data-Dumper virtual/perl-Exporter virtual/perl-File-Path virtual/perl-File-Spec virtual/perl-File-Temp virtual/perl-Getopt-Long virtual/perl-Scalar-List-Utils virtual/perl-Time-HiRes mpi? ( virtual/mpi ) -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=http://meme-suite.org/meme-software/4.11.2/meme_4.11.2.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 estack 43ddf5aaffa7a8d0482df54d25a66a1f libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=a4080439675628436c06de8db9f59c6e diff --git a/metadata/md5-cache/sci-biology/mira-4.0.2 b/metadata/md5-cache/sci-biology/mira-4.0.2 deleted file mode 100644 index c3ab2984c38f..000000000000 --- a/metadata/md5-cache/sci-biology/mira-4.0.2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install postinst prepare -DEPEND=dev-libs/boost[threads] dev-util/google-perftools sys-devel/flex app-editors/vim-core dev-libs/expat >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina -EAPI=6 -HOMEPAGE=http://www.chevreux.org/projects_mira.html -IUSE=doc -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x86-macos -LICENSE=GPL-2 -RDEPEND=dev-libs/boost[threads] dev-util/google-perftools -SLOT=0 -SRC_URI=https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0.2.tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_06-07-2012.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=4e9fc8a550640febbc0b71544c16618c diff --git a/metadata/md5-cache/sci-biology/mosaik-2.2.30 b/metadata/md5-cache/sci-biology/mosaik-2.2.30 deleted file mode 100644 index 2b31348a3ea9..000000000000 --- a/metadata/md5-cache/sci-biology/mosaik-2.2.30 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile configure install unpack -DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies -EAPI=6 -HOMEPAGE=https://github.com/wanpinglee/MOSAIK -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> mosaik-2.2.30.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf vcs-snapshot 3be1ab44131e8c0bbdaa75823008444b -_md5_=630686b35f8a549c580c5fd0e2cb02fc diff --git a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 deleted file mode 100644 index bb76d8a95324..000000000000 --- a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare setup -DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) app-arch/unzip virtual/fortran -DESCRIPTION=A suite of algorithms for ecological bioinformatics -EAPI=5 -HOMEPAGE=https://www.mothur.org/ -IUSE=mpi +readline -KEYWORDS=amd64 x86 -LICENSE=GPL-3 -RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran -SLOT=0 -SRC_URI=https://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 fortran-2 9e7f20c99213f0627ff7f873d4aaa25d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=17f8b3c73710bbb746fc4cbfcf78b85d diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 deleted file mode 100644 index dd5bd27cc2f2..000000000000 --- a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) -DESCRIPTION=Bayesian Inference of Phylogeny -EAPI=4 -HOMEPAGE=http://mrbayes.csit.fsu.edu/ -IUSE=debug mpi readline -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=GPL-2 -RDEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) -SLOT=0 -SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=a082c9b1f1b5f9fa9b85e23eb7009a6d diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 deleted file mode 100644 index 8cdce0ea72ba..000000000000 --- a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) -DESCRIPTION=Bayesian Inference of Phylogeny -EAPI=5 -HOMEPAGE=http://mrbayes.csit.fsu.edu/ -IUSE=debug mpi readline -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=GPL-2 -RDEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) -SLOT=0 -SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=a944448f568e57bb9f221cd1f437ab09 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23 b/metadata/md5-cache/sci-biology/mummer-3.23 deleted file mode 100644 index 46151624c2bb..000000000000 --- a/metadata/md5-cache/sci-biology/mummer-3.23 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=A rapid whole genome aligner -EAPI=6 -HOMEPAGE=http://mummer.sourceforge.net/ -IUSE=doc -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=app-shells/tcsh dev-lang/perl -SLOT=0 -SRC_URI=mirror://sourceforge/mummer/MUMmer3.23.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=c256f298b416306c1be7005e7877f7b9 diff --git a/metadata/md5-cache/sci-biology/muscle-3.8.31 b/metadata/md5-cache/sci-biology/muscle-3.8.31 deleted file mode 100644 index 4e5e149ac328..000000000000 --- a/metadata/md5-cache/sci-biology/muscle-3.8.31 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=Multiple sequence comparison by log-expectation -EAPI=5 -HOMEPAGE=http://www.drive5.com/muscle/ -KEYWORDS=amd64 ppc x86 -LICENSE=public-domain -RDEPEND=!sci-libs/libmuscle -SLOT=0 -SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=500ff424aff8c56744362bc87a3ff285 diff --git a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 deleted file mode 100644 index 04c9fa3b90c9..000000000000 --- a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare setup -DEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) -DESCRIPTION=Development toolkit and applications for computational biology, including BLAST -EAPI=5 -HOMEPAGE=https://www.ncbi.nlm.nih.gov/ -IUSE=doc static-libs X -KEYWORDS=~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=public-domain -RDEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) -SLOT=0 -SRC_URI=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/ncbi.tar.gz -> ncbi-tools-2.2.26.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=550e2f5b19e400b1ca82a7ba4f7bd44a diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6 b/metadata/md5-cache/sci-biology/newick-utils-1.6 deleted file mode 100644 index f9cdb1fd46cd..000000000000 --- a/metadata/md5-cache/sci-biology/newick-utils-1.6 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=test -DESCRIPTION=Tools for processing phylogenetic trees -EAPI=6 -HOMEPAGE=http://cegg.unige.ch/newick_utils -KEYWORDS=~amd64 ~x86 -LICENSE=BSD -RDEPEND=!dev-games/libnw -SLOT=0 -SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz -_md5_=f70356a582d317400bf4cd17b73beb16 diff --git a/metadata/md5-cache/sci-biology/njplot-2.3-r2 b/metadata/md5-cache/sci-biology/njplot-2.3-r2 deleted file mode 100644 index 3eab09436b34..000000000000 --- a/metadata/md5-cache/sci-biology/njplot-2.3-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu -DESCRIPTION=A phylogenetic tree drawing program which supports tree rooting -EAPI=6 -HOMEPAGE=http://pbil.univ-lyon1.fr/software/njplot.html -KEYWORDS=~amd64 ~x86 -LICENSE=public-domain -RDEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu -SLOT=0 -SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-2.3.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=c70b49c7f5e1a92f5169df372f9638c6 diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r1 b/metadata/md5-cache/sci-biology/pals-1.0-r1 deleted file mode 100644 index c1ca8de69a5e..000000000000 --- a/metadata/md5-cache/sci-biology/pals-1.0-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Pairwise Aligner for Long Sequences -EAPI=6 -HOMEPAGE=http://www.drive5.com/pals/ -KEYWORDS=amd64 x86 -LICENSE=public-domain -SLOT=0 -SRC_URI=http://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=b0df20d47905df6a290c5fe2f79fd48b diff --git a/metadata/md5-cache/sci-biology/paml-4.4c-r1 b/metadata/md5-cache/sci-biology/paml-4.4c-r1 deleted file mode 100644 index b1b9e039c32a..000000000000 --- a/metadata/md5-cache/sci-biology/paml-4.4c-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood -EAPI=5 -HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html -KEYWORDS=amd64 x86 -LICENSE=free-noncomm -SLOT=0 -SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.4c.tar.gz -_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=c46d709378282d4ccbb567aaa00ee01a diff --git a/metadata/md5-cache/sci-biology/phrap-1.080812-r2 b/metadata/md5-cache/sci-biology/phrap-1.080812-r2 deleted file mode 100644 index ab42e7852a47..000000000000 --- a/metadata/md5-cache/sci-biology/phrap-1.080812-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install nofetch -DESCRIPTION=Shotgun assembly and alignment utilities -EAPI=6 -HOMEPAGE=http://www.phrap.org/ -KEYWORDS=~amd64 ~x86 -LICENSE=phrap -RDEPEND=dev-lang/perl dev-perl/Tk -RESTRICT=fetch -SLOT=0 -SRC_URI=phrap-1.080812-distrib.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=e72f3e08accb23ebf55562689dad5f46 diff --git a/metadata/md5-cache/sci-biology/phred-071220-r1 b/metadata/md5-cache/sci-biology/phred-071220-r1 deleted file mode 100644 index 6b7893cd8fd6..000000000000 --- a/metadata/md5-cache/sci-biology/phred-071220-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install nofetch -DESCRIPTION=A base caller for Sanger DNA sequencing -EAPI=6 -HOMEPAGE=http://phrap.org/phredphrapconsed.html -KEYWORDS=~amd64 ~x86 -LICENSE=phrap -RESTRICT=fetch -SLOT=0 -SRC_URI=phred-dist-071220.b-acd.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=92065ca72fd55796ea38e3d5ae9ee8b8 diff --git a/metadata/md5-cache/sci-biology/phylip-3.69-r1 b/metadata/md5-cache/sci-biology/phylip-3.69-r1 deleted file mode 100644 index 4acb8033a5b3..000000000000 --- a/metadata/md5-cache/sci-biology/phylip-3.69-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=x11-libs/libXaw x11-base/xorg-proto -DESCRIPTION=The PHYLogeny Inference Package -EAPI=5 -HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html -KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=freedist -RDEPEND=x11-libs/libXaw -SLOT=0 -SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=d0432dd24ac4208e4dfcf91bea60d018 diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r1 b/metadata/md5-cache/sci-biology/phylip-3.696-r1 deleted file mode 100644 index cf3162ed87c1..000000000000 --- a/metadata/md5-cache/sci-biology/phylip-3.696-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=x11-libs/libXaw x11-base/xorg-proto -DESCRIPTION=The PHYLogeny Inference Package -EAPI=5 -HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html -KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=BSD-2 -RDEPEND=x11-libs/libXaw -SLOT=0 -SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=8b5da2d13bfc622e3156ee011204f899 diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r2 b/metadata/md5-cache/sci-biology/phylip-3.696-r2 deleted file mode 100644 index 95ebdd29ef73..000000000000 --- a/metadata/md5-cache/sci-biology/phylip-3.696-r2 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=x11-libs/libXaw !!dev-lang/elixir x11-base/xorg-proto -DESCRIPTION=The PHYLogeny Inference Package -EAPI=5 -HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html -KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=BSD-2 -RDEPEND=x11-libs/libXaw !!dev-lang/elixir -SLOT=0 -SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=69a57b901c6c154707c8c45f5ba39189 diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 deleted file mode 100644 index 0e2987bcb5fc..000000000000 --- a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=Estimation of large phylogenies by maximum likelihood -EAPI=6 -HOMEPAGE=http://atgc.lirmm.fr/phyml/ -KEYWORDS=amd64 ppc x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=fcca6fb4f9e88f5eb6a63a3ee0c79df7 diff --git a/metadata/md5-cache/sci-biology/picard-1.103 b/metadata/md5-cache/sci-biology/picard-1.103 deleted file mode 100644 index da6c03440e16..000000000000 --- a/metadata/md5-cache/sci-biology/picard-1.103 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install preinst prepare setup test -DEPEND=>=virtual/jdk-1.6 dev-java/ant-apache-bcel:0 test? ( dev-java/testng:0 dev-lang/R ) dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip ) >=dev-java/ant-core-1.8.2:0 dev-java/ant-apache-bcel dev-java/testng:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 -DESCRIPTION=Java-based command-line utilities that manipulate SAM files -EAPI=5 -HOMEPAGE=http://picard.sourceforge.net/ -IUSE=elibc_FreeBSD doc source test elibc_FreeBSD -KEYWORDS=~amd64 ~x86 -LICENSE=Apache-2.0 -RDEPEND=>=virtual/jre-1.6 dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip ) -SLOT=0 -SRC_URI=https://dev.gentoo.org/~ercpe/distfiles/sci-biology/picard/picard-1.103.tar.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=09627e6bb74ee9997324bde01a56bcbd diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r1 b/metadata/md5-cache/sci-biology/piler-1.0-r1 deleted file mode 100644 index fb99a6194a89..000000000000 --- a/metadata/md5-cache/sci-biology/piler-1.0-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Analysis of repetitive DNA found in genome sequences -EAPI=6 -HOMEPAGE=http://www.drive5.com/piler/ -KEYWORDS=amd64 x86 -LICENSE=public-domain -RDEPEND=|| ( sci-biology/muscle sci-libs/libmuscle ) sci-biology/pals -SLOT=0 -SRC_URI=http://www.drive5.com/piler/piler_source.tar.gz -> piler-1.0.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=7b5a6d618aac08240cf165a04509c319 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 b/metadata/md5-cache/sci-biology/pilercr-1.0-r1 deleted file mode 100644 index 9a3239fe1d5f..000000000000 --- a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) -EAPI=6 -HOMEPAGE=http://www.drive5.com/pilercr/ -KEYWORDS=amd64 x86 -LICENSE=public-domain -SLOT=0 -SRC_URI=http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> pilercr-1.0.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=d9f7901d3776c424cfb93782cc6ddafa diff --git a/metadata/md5-cache/sci-biology/plink-1.07-r1 b/metadata/md5-cache/sci-biology/plink-1.07-r1 deleted file mode 100644 index cb33634847cc..000000000000 --- a/metadata/md5-cache/sci-biology/plink-1.07-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=app-arch/unzip lapack? ( virtual/pkgconfig ) -DESCRIPTION=Whole genome association analysis toolset -EAPI=4 -HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ -IUSE=lapack -webcheck R -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib lapack? ( virtual/lapack ) -SLOT=0 -SRC_URI=http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=b659cc5ab8af123ceaf15f1349214345 diff --git a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 deleted file mode 100644 index e6a25114c67e..000000000000 --- a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=app-arch/unzip virtual/pkgconfig -DESCRIPTION=Whole genome association analysis toolset -EAPI=5 -HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib virtual/cblas virtual/lapack -SLOT=0 -SRC_URI=http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> plink-1.90_pre140514.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=570249dc23feeff7b47b3e81df358196 diff --git a/metadata/md5-cache/sci-biology/poa-2-r1 b/metadata/md5-cache/sci-biology/poa-2-r1 deleted file mode 100644 index 4e911ec2aa18..000000000000 --- a/metadata/md5-cache/sci-biology/poa-2-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Fast multiple sequence alignments using partial-order graphs -EAPI=5 -HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/ -IUSE=static-libs -KEYWORDS=~x86 ~amd64 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=4f0b8d6c2192465644af4890a995d48a diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603 deleted file mode 100644 index 16126944bac3..000000000000 --- a/metadata/md5-cache/sci-biology/prank-140603 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Probabilistic Alignment Kit -EAPI=6 -HOMEPAGE=http://wasabiapp.org/software/prank/ -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -SLOT=0 -SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=17023476000980284365a9c0ed04a6f0 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.7 b/metadata/md5-cache/sci-biology/primer3-2.3.7 deleted file mode 100644 index adbd3096ef58..000000000000 --- a/metadata/md5-cache/sci-biology/primer3-2.3.7 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=dev-lang/perl -DESCRIPTION=Primer Design for PCR reactions -EAPI=6 -HOMEPAGE=http://primer3.sourceforge.net/ -KEYWORDS=~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=GPL-2 -SLOT=0 -SRC_URI=mirror://sourceforge/project/primer3/primer3/2.3.7/primer3-2.3.7.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=e79ee4774138e651c83467c2b2cb2926 diff --git a/metadata/md5-cache/sci-biology/prints-39.0-r1 b/metadata/md5-cache/sci-biology/prints-39.0-r1 deleted file mode 100644 index 31cee51db19f..000000000000 --- a/metadata/md5-cache/sci-biology/prints-39.0-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( sci-biology/emboss ) -DESCRIPTION=A protein motif fingerprint database -EAPI=6 -HOMEPAGE=http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=emboss? ( sci-biology/emboss ) -SLOT=0 -SRC_URI=mirror://gentoo/prints-39.0.tar.bz2 -_md5_=03843bbc5bed197d8df7a7bbc970230a diff --git a/metadata/md5-cache/sci-biology/probcons-1.12-r1 b/metadata/md5-cache/sci-biology/probcons-1.12-r1 deleted file mode 100644 index 3c193632a5db..000000000000 --- a/metadata/md5-cache/sci-biology/probcons-1.12-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences -EAPI=5 -HOMEPAGE=http://probcons.stanford.edu/ -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot -SLOT=0 -SRC_URI=http://probcons.stanford.edu/probcons_v1_12.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=19a24bd3c543d599d5b3392e66b7022e diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3 b/metadata/md5-cache/sci-biology/prodigal-2.6.3 deleted file mode 100644 index f92b89c227a6..000000000000 --- a/metadata/md5-cache/sci-biology/prodigal-2.6.3 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure -DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm -EAPI=6 -HOMEPAGE=http://prodigal.ornl.gov/ -KEYWORDS=~amd64 -LICENSE=GPL-3 -SLOT=0 -SRC_URI=https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz -> prodigal-2.6.3.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=9cea3bcc55e864076d7e4b542f657f96 diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.39 b/metadata/md5-cache/sci-biology/profphd-1.0.39 deleted file mode 100644 index d72071f109f3..000000000000 --- a/metadata/md5-cache/sci-biology/profphd-1.0.39 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=dev-lang/perl -DESCRIPTION=Secondary structure and solvent accessibility predictor -EAPI=5 -HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=GPL-2 -RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils -SLOT=0 -SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.39.tar.xz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=8e866cc812e134cdc7a7837e5b60aa21 diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.40 b/metadata/md5-cache/sci-biology/profphd-1.0.40 deleted file mode 100644 index 50f84b8140b4..000000000000 --- a/metadata/md5-cache/sci-biology/profphd-1.0.40 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=dev-lang/perl -DESCRIPTION=Secondary structure and solvent accessibility predictor -EAPI=5 -HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=GPL-2 -RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils -SLOT=0 -SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.40.tar.xz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=b641a6cfd444fa4b83d5963246948636 diff --git a/metadata/md5-cache/sci-biology/prosite-2017.02 b/metadata/md5-cache/sci-biology/prosite-2017.02 deleted file mode 100644 index ccabbc4a37bb..000000000000 --- a/metadata/md5-cache/sci-biology/prosite-2017.02 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( sci-biology/emboss ) -DESCRIPTION=A protein families and domains database -EAPI=6 -HOMEPAGE=https://prosite.expasy.org/ -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=swiss-prot -RDEPEND=emboss? ( sci-biology/emboss ) -SLOT=0 -SRC_URI=ftp://ftp.expasy.org/databases/prosite/old_releases/prosite2017_02.tar.bz2 -_md5_=e37bd9f81e9458715d22a6138fb2029a diff --git a/metadata/md5-cache/sci-biology/psipred-3.2.1 b/metadata/md5-cache/sci-biology/psipred-3.2.1 deleted file mode 100644 index c85593c128c3..000000000000 --- a/metadata/md5-cache/sci-biology/psipred-3.2.1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Protein Secondary Structure Prediction -EAPI=4 -HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ -IUSE=test -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=psipred -RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) -SLOT=0 -SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred321.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=bf7aa50ff789d669fe4846e0e41828d7 diff --git a/metadata/md5-cache/sci-biology/psipred-3.3 b/metadata/md5-cache/sci-biology/psipred-3.3 deleted file mode 100644 index d2087ae3d6f7..000000000000 --- a/metadata/md5-cache/sci-biology/psipred-3.3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Protein Secondary Structure Prediction -EAPI=4 -HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ -IUSE=test -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=psipred -RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) -SLOT=0 -SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.3.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=d719359ecbbd5c0825e93788cc4f0af1 diff --git a/metadata/md5-cache/sci-biology/psipred-3.4 b/metadata/md5-cache/sci-biology/psipred-3.4 deleted file mode 100644 index d60214127cf0..000000000000 --- a/metadata/md5-cache/sci-biology/psipred-3.4 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Protein Secondary Structure Prediction -EAPI=5 -HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ -IUSE=test -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=psipred -RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) -SLOT=0 -SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.4.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=671e20dbd509ebdd9e9c492e2c53b6a1 diff --git a/metadata/md5-cache/sci-biology/psipred-3.5 b/metadata/md5-cache/sci-biology/psipred-3.5 deleted file mode 100644 index b55a418b2480..000000000000 --- a/metadata/md5-cache/sci-biology/psipred-3.5 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DESCRIPTION=Protein Secondary Structure Prediction -EAPI=5 -HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ -IUSE=test -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=psipred -RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) -SLOT=0 -SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.5.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=671e20dbd509ebdd9e9c492e2c53b6a1 diff --git a/metadata/md5-cache/sci-biology/pysam-0.12.0.1 b/metadata/md5-cache/sci-biology/pysam-0.12.0.1 deleted file mode 100644 index d83a6de11f15..000000000000 --- a/metadata/md5-cache/sci-biology/pysam-0.12.0.1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND==sci-libs/htslib-1.5*:= dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format -EAPI=6 -HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/ -IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 -KEYWORDS=~amd64 ~x86 -LICENSE=MIT -RDEPEND==sci-libs/htslib-1.5*:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] -REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) -SLOT=0 -SRC_URI=mirror://pypi/p/pysam/pysam-0.12.0.1.tar.gz -_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=c02049dd445007999f7534a8e5d17656 diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 deleted file mode 100644 index d7019e7fcb07..000000000000 --- a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=dev-lang/perl sci-biology/hmmer:2 -DESCRIPTION=Prototype ncRNA genefinder -EAPI=6 -HOMEPAGE=http://selab.janelia.org/software.html -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=dev-lang/perl sci-biology/hmmer:2 -SLOT=0 -SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2 -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=0fc8dac0f54d22c60da996470b3b33ee diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-7.2.6 deleted file mode 100644 index d71204ce3c6a..000000000000 --- a/metadata/md5-cache/sci-biology/raxml-7.2.6 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees -EAPI=5 -HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html -IUSE=cpu_flags_x86_sse3 +threads -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -REQUIRED_USE=cpu_flags_x86_sse3 -SLOT=0 -SRC_URI=http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.6.tar.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=f2b8e0b4e5701d9b20bcbf9151c9b868 diff --git a/metadata/md5-cache/sci-biology/rebase-1701 b/metadata/md5-cache/sci-biology/rebase-1701 deleted file mode 100644 index d86bf89d9ab9..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1701 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1701.tar.xz -_md5_=68457638d36f4995a29fb959283e85a4 diff --git a/metadata/md5-cache/sci-biology/rebase-1702 b/metadata/md5-cache/sci-biology/rebase-1702 deleted file mode 100644 index b16c62f4e2fa..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1702 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1702.tar.xz -_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1703 b/metadata/md5-cache/sci-biology/rebase-1703 deleted file mode 100644 index 5172f9e323ca..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1703 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1703.tar.xz -_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1704 b/metadata/md5-cache/sci-biology/rebase-1704 deleted file mode 100644 index 4165b701add8..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1704 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1704.tar.xz -_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1803 b/metadata/md5-cache/sci-biology/rebase-1803 deleted file mode 100644 index e04f8ae6b53d..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1803 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1803.tar.xz -_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/rebase-1806 b/metadata/md5-cache/sci-biology/rebase-1806 deleted file mode 100644 index 8eeafd55e477..000000000000 --- a/metadata/md5-cache/sci-biology/rebase-1806 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -DESCRIPTION=A restriction enzyme database -EAPI=6 -HOMEPAGE=http://rebase.neb.com -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris -LICENSE=public-domain -RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) -RESTRICT=binchecks strip -SLOT=0 -SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1806.tar.xz -_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08 deleted file mode 100644 index 47eba7fb8c90..000000000000 --- a/metadata/md5-cache/sci-biology/recon-1.08 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Automated de novo identification of repeat families from genomic sequences -EAPI=6 -HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html -IUSE=examples -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=dev-lang/perl -SLOT=0 -SRC_URI=http://www.repeatmasker.org/RECON-1.08.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=2ddd537d912c7c88b6f0b0d203a51613 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 deleted file mode 100644 index dd6911f77a84..000000000000 --- a/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Screen DNA sequences for interspersed repeats and low complexity DNA -EAPI=5 -HOMEPAGE=http://repeatmasker.org/ -KEYWORDS=~amd64 ~x86 -LICENSE=OSL-2.1 -RDEPEND=sci-biology/rmblast sci-biology/trf sci-biology/repeatmasker-libraries -SLOT=0 -SRC_URI=http://www.repeatmasker.org/RepeatMasker-open-4-0-1.tar.gz -_md5_=9dc3465c819cad44a5a8175a267222d4 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 deleted file mode 100644 index 3f4cf1c19817..000000000000 --- a/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install nofetch -DESCRIPTION=A special version of RepBase used by RepeatMasker -EAPI=5 -HOMEPAGE=http://repeatmasker.org/ -KEYWORDS=~amd64 ~x86 -LICENSE=all-rights-reserved -RESTRICT=fetch -SLOT=0 -SRC_URI=repeatmaskerlibraries-20120418.tar.gz -_md5_=0cb0252babed9e448a9b2b06eaa2220c diff --git a/metadata/md5-cache/sci-biology/rmblast-1.2-r1 b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 deleted file mode 100644 index 84990ee30ed3..000000000000 --- a/metadata/md5-cache/sci-biology/rmblast-1.2-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=dev-libs/boost app-arch/cpio -DESCRIPTION=RepeatMasker compatible version of NCBI BLAST+ -EAPI=5 -HOMEPAGE=http://www.repeatmasker.org/RMBlast.html -KEYWORDS=~amd64 ~x86 -LICENSE=OSL-2.1 -RDEPEND=dev-libs/boost -SLOT=0 -SRC_URI=http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz https://dev.gentoo.org/~mgorny/dist/rmblast-1.2-gcc47.patch.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=1283e94bf3a231a794a498d2769aaa7d diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 deleted file mode 100644 index f0e81c01d7d9..000000000000 --- a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions -EAPI=6 -HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html -KEYWORDS=~amd64 ~x86 -LICENSE=public-domain -SLOT=0 -SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=788c156d45287bef4f6aa876055bde4c diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 b/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 deleted file mode 100644 index 12896fc220d1..000000000000 --- a/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare setup -DEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] sys-libs/ncurses:0= dev-lang/perl virtual/pkgconfig -DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats -EAPI=6 -HOMEPAGE=http://samtools.sourceforge.net/ -IUSE=examples python_targets_python2_7 -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos -LICENSE=MIT -RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] sys-libs/ncurses:0= dev-lang/perl -REQUIRED_USE=python_targets_python2_7 -SLOT=0.1-legacy -SRC_URI=https://github.com/samtools/samtools/archive/0.1.20.tar.gz -> samtools-0.1.20.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=fa48f0b2be780a9264eb9d727ec53335 diff --git a/metadata/md5-cache/sci-biology/samtools-1.5 b/metadata/md5-cache/sci-biology/samtools-1.5 deleted file mode 100644 index 6d3d095a74c9..000000000000 --- a/metadata/md5-cache/sci-biology/samtools-1.5 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=install prepare test -DEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats -EAPI=6 -HOMEPAGE=http://www.htslib.org/ -IUSE=examples python_targets_python2_7 -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos -LICENSE=MIT -RDEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] -REQUIRED_USE=|| ( python_targets_python2_7 ) -SLOT=0 -SRC_URI=mirror://sourceforge/samtools/samtools-1.5.tar.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=8d92b4a814f62eab87bac2be22c2470c diff --git a/metadata/md5-cache/sci-biology/seaview-4.3.5 b/metadata/md5-cache/sci-biology/seaview-4.3.5 deleted file mode 100644 index f0dfa48c04a0..000000000000 --- a/metadata/md5-cache/sci-biology/seaview-4.3.5 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig -DESCRIPTION=A graphical multiple sequence alignment editor -EAPI=5 -HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html -IUSE=+xft -KEYWORDS=amd64 x86 -LICENSE=public-domain -RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml -SLOT=0 -SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.3.5.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.5.4 b/metadata/md5-cache/sci-biology/seaview-4.5.4 deleted file mode 100644 index 969930293946..000000000000 --- a/metadata/md5-cache/sci-biology/seaview-4.5.4 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig -DESCRIPTION=A graphical multiple sequence alignment editor -EAPI=5 -HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html -IUSE=+xft -KEYWORDS=amd64 x86 -LICENSE=public-domain -RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml -SLOT=0 -SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.4.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.6 b/metadata/md5-cache/sci-biology/seaview-4.6 deleted file mode 100644 index b71aeb30d146..000000000000 --- a/metadata/md5-cache/sci-biology/seaview-4.6 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml virtual/pkgconfig -DESCRIPTION=A graphical multiple sequence alignment editor -EAPI=6 -HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html -IUSE=+xft -KEYWORDS=~amd64 ~x86 -LICENSE=public-domain -RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml -SLOT=0 -SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=1a6723f1ab0e67cc0d63dd54a902900f diff --git a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 deleted file mode 100644 index 4947ba4bf84b..000000000000 --- a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install postinst prepare setup test -DEPEND=app-arch/bzip2 sys-libs/zlib test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=C++ Sequence Analysis Library -EAPI=6 -HOMEPAGE=http://www.seqan.de/ -IUSE=cpu_flags_x86_sse4_1 test -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=BSD GPL-3 -RDEPEND=app-arch/bzip2 sys-libs/zlib -REQUIRED_USE=cpu_flags_x86_sse4_1 -SLOT=1.4 -SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-1.4.2.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=1b7be060ecec73f1e66596a71b90a92a diff --git a/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 b/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 deleted file mode 100644 index 76c7559b5406..000000000000 --- a/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test -DEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=C++ Sequence Analysis Library -EAPI=6 -HOMEPAGE=http://www.seqan.de/ -IUSE=cpu_flags_x86_sse4_1 doc test -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=BSD GPL-3 -RDEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 -REQUIRED_USE=cpu_flags_x86_sse4_1 -SLOT=0 -SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-2.2.0.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=aaf78a04252c5e6c2b92b04c7211b73c diff --git a/metadata/md5-cache/sci-biology/seqan-2.4.0 b/metadata/md5-cache/sci-biology/seqan-2.4.0 deleted file mode 100644 index 4fb11d2bfa86..000000000000 --- a/metadata/md5-cache/sci-biology/seqan-2.4.0 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test -DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 -DESCRIPTION=C++ Sequence Analysis Library -EAPI=6 -HOMEPAGE=http://www.seqan.de/ -IUSE=cpu_flags_x86_sse4_1 doc tools -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=BSD GPL-3 -RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 -REQUIRED_USE=cpu_flags_x86_sse4_1 -SLOT=0 -SRC_URI=https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=ca34cde2b2fc2f8692469a016bc077f6 diff --git a/metadata/md5-cache/sci-biology/seqan-9999 b/metadata/md5-cache/sci-biology/seqan-9999 deleted file mode 100644 index 10310a95c374..000000000000 --- a/metadata/md5-cache/sci-biology/seqan-9999 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare setup test unpack -DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] -DESCRIPTION=C++ Sequence Analysis Library -EAPI=6 -HOMEPAGE=http://www.seqan.de/ -IUSE=cpu_flags_x86_sse4_1 doc tools -LICENSE=BSD GPL-3 -RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 -REQUIRED_USE=cpu_flags_x86_sse4_1 -SLOT=0 -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=954c2a9b05e60f6a61eb27c1cc720117 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.0.1 b/metadata/md5-cache/sci-biology/shrimp-2.0.1 deleted file mode 100644 index 09c3c171924f..000000000000 --- a/metadata/md5-cache/sci-biology/shrimp-2.0.1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare setup -DEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs -DESCRIPTION=SHort Read Mapping Package -EAPI=4 -HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ -IUSE=custom-cflags -KEYWORDS=amd64 x86 -LICENSE=shrimp -RDEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs -SLOT=0 -SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_0_1.src.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=33caa30e4cdcb3e86f4b1be8c6c30c46 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.2.3 b/metadata/md5-cache/sci-biology/shrimp-2.2.3 deleted file mode 100644 index aaf618a0e1e6..000000000000 --- a/metadata/md5-cache/sci-biology/shrimp-2.2.3 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile install prepare pretend setup -DEPEND=!sci-mathematics/cado-nfs -DESCRIPTION=SHort Read Mapping Package -EAPI=5 -HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ -IUSE=custom-cflags +cpu_flags_x86_sse2 python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=shrimp -RDEPEND=!sci-mathematics/cado-nfs python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_3.src.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=98a7a2b9765ad5e245b1b7b9be67060b diff --git a/metadata/md5-cache/sci-biology/sibsim4-0.20 b/metadata/md5-cache/sci-biology/sibsim4-0.20 deleted file mode 100644 index dce86b046849..000000000000 --- a/metadata/md5-cache/sci-biology/sibsim4-0.20 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=A rewrite and improvement upon sim4, a DNA-mRNA aligner -EAPI=5 -HOMEPAGE=http://sibsim4.sourceforge.net/ -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=mirror://sourceforge/sibsim4/SIBsim4-0.20.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=84a29c8972011ec4b86f3c8235a7b5d2 diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r2 b/metadata/md5-cache/sci-biology/sim4-20030921-r2 deleted file mode 100644 index 6d0cdfcf5f81..000000000000 --- a/metadata/md5-cache/sci-biology/sim4-20030921-r2 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=A program to align cDNA and genomic DNA -EAPI=6 -HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html -KEYWORDS=~amd64 ~ppc ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=fca00baca723bafd7976eff8dccc5c26 diff --git a/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 deleted file mode 100644 index eee0b602f033..000000000000 --- a/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=dev-libs/boost:= >=sys-devel/autoconf-archive-2016.09.16 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A library and API for manipulating large SNP datasets -EAPI=6 -HOMEPAGE=http://www.birc.au.dk/~mailund/SNPFile/ -IUSE=static-libs -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -RDEPEND=dev-libs/boost:= -SLOT=0 -SRC_URI=http://www.birc.au.dk/~mailund/SNPFile/download/snpfile-2.0.1.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=7c64014825a157024d03614c037abcfc diff --git a/metadata/md5-cache/sci-biology/stride-20011129-r1 b/metadata/md5-cache/sci-biology/stride-20011129-r1 deleted file mode 100644 index e3aa3af0fd8f..000000000000 --- a/metadata/md5-cache/sci-biology/stride-20011129-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=Protein secondary structure assignment from atomic coordinates -EAPI=5 -HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ -KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos -LICENSE=STRIDE -RESTRICT=mirror bindist -SLOT=0 -SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz https://dev.gentoo.org/~jlec/distfiles/stride-20060723-update.patch.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=d73db26f06440dc2c2a1e25befe5d490 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 deleted file mode 100644 index 5ada2e982e45..000000000000 --- a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=A multiple sequence alignment package -EAPI=6 -HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html -KEYWORDS=~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux -LICENSE=GPL-2 -RDEPEND=sci-biology/clustalw sci-chemistry/tm-align -SLOT=0 -SRC_URI=http://www.tcoffee.org/Packages/Beta/Latest/T-COFFEE_distribution_Version_11.00.4466924.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=5c54b109c5b8bef93adbc5f99ddd7114 diff --git a/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 b/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 deleted file mode 100644 index 9ff36ab36e55..000000000000 --- a/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install postinst prepare setup -DEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 virtual/pkgconfig sci-biology/seqan:1.4 >=sys-devel/autoconf-archive-2016.09.16 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Python-based splice junction mapper for RNA-Seq reads using bowtie2 -EAPI=6 -HOMEPAGE=https://ccb.jhu.edu/software/tophat/ -IUSE=debug python_targets_python2_7 -KEYWORDS=~amd64 ~x86 -LICENSE=Artistic -RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),python_single_target_python2_7(+)] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 -REQUIRED_USE=python_targets_python2_7 -SLOT=0 -SRC_URI=https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 ffa9c3284c6b07b8c9f7933911f63812 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=efee8069c83c578acac8e57b429ad985 diff --git a/metadata/md5-cache/sci-biology/transfac-3.2-r1 b/metadata/md5-cache/sci-biology/transfac-3.2-r1 deleted file mode 100644 index 91dec5eae8be..000000000000 --- a/metadata/md5-cache/sci-biology/transfac-3.2-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install -DEPEND=emboss? ( sci-biology/emboss ) -DESCRIPTION=A database of eucaryotic transcription factors -EAPI=6 -HOMEPAGE=http://www.gene-regulation.com/pub/databases.html -IUSE=emboss minimal -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=emboss? ( sci-biology/emboss ) -SLOT=3 -SRC_URI=ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z -_md5_=d8fcea543b5af9fc877c63800e1bd6d3 diff --git a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 deleted file mode 100644 index c096695590e7..000000000000 --- a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install prepare setup -DEPEND=mpi? ( virtual/mpi ) -DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data -EAPI=4 -HOMEPAGE=http://www.tree-puzzle.de -IUSE=mpi -KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos -LICENSE=GPL-2 -RDEPEND=mpi? ( virtual/mpi ) -RESTRICT=test -SLOT=0 -SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=6f933fde60eb23f0e50fbe5e137bbc7e diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 deleted file mode 100644 index 119076c2f725..000000000000 --- a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=x11-libs/wxGTK:3.0[X] >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=A phylogenetic tree viewer -EAPI=5 -HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=x11-libs/wxGTK:3.0[X] -SLOT=0 -SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf wxwidgets 04e063b0eff26daaea83d859dd9d6e05 -_md5_=ce129f3e61a849cfd3654e5a9fa4b17a diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r1 b/metadata/md5-cache/sci-biology/trf-4.04-r1 deleted file mode 100644 index 3195b5c5feec..000000000000 --- a/metadata/md5-cache/sci-biology/trf-4.04-r1 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install unpack -DESCRIPTION=Tandem Repeats Finder -EAPI=6 -HOMEPAGE=http://tandem.bu.edu/trf/trf.html -KEYWORDS=amd64 x86 -LICENSE=trf -RESTRICT=mirror bindist -SLOT=0 -SRC_URI=http://tandem.bu.edu/trf/downloads/trf404.linux -_md5_=51a51c14c6646aaa7d7494d561535729 diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.31 b/metadata/md5-cache/sci-biology/trnascan-se-1.31 deleted file mode 100644 index 5a2f4fc6e741..000000000000 --- a/metadata/md5-cache/sci-biology/trnascan-se-1.31 +++ /dev/null @@ -1,10 +0,0 @@ -DEFINED_PHASES=install prepare test -DESCRIPTION=tRNA detection in large-scale genome sequences -EAPI=6 -HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> trnascan-se-1.31.tar.gz -_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=3f4bcdf31fe276f90a95e2f4b311deae diff --git a/metadata/md5-cache/sci-biology/uchime-4.2.40 b/metadata/md5-cache/sci-biology/uchime-4.2.40 deleted file mode 100644 index daffc0c3042f..000000000000 --- a/metadata/md5-cache/sci-biology/uchime-4.2.40 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test -DEPEND=sys-devel/make >=dev-util/cmake-3.9.6 -DESCRIPTION=Fast, accurate chimera detection -EAPI=6 -HOMEPAGE=http://www.drive5.com/uchime/ -IUSE=debug -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -SLOT=0 -SRC_URI=http://drive5.com/uchime/uchime4.2.40_src.tar.gz -_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 -_md5_=6adcbb8c658bdc3c40f797c61f5c58b0 diff --git a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 deleted file mode 100644 index 2597f362c85e..000000000000 --- a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare prerm setup -DEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 -DESCRIPTION=The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath -EAPI=5 -HOMEPAGE=http://genome.ucsc.edu/ -IUSE=+mysql +server static-libs vhosts -KEYWORDS=~amd64 ~x86 -LICENSE=blat -RDEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 -REQUIRED_USE=server? ( mysql ) -SLOT=0 -SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 6ae2395d7f341093c36057cb4f69101a -_md5_=e8bc8c4496d6c751b8f8452324e059f4 diff --git a/metadata/md5-cache/sci-biology/unafold-3.8-r1 b/metadata/md5-cache/sci-biology/unafold-3.8-r1 deleted file mode 100644 index e175b285bf25..000000000000 --- a/metadata/md5-cache/sci-biology/unafold-3.8-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=prepare -DESCRIPTION=Unified Nucleic Acid Folding and hybridization package -EAPI=5 -HOMEPAGE=http://mfold.rna.albany.edu/ -IUSE=custom-cflags -KEYWORDS=~amd64 ~x86 -LICENSE=unafold -SLOT=0 -SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=f6e357557efc2f86eab0adadd32142ce diff --git a/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 deleted file mode 100644 index 3e9a8b5e2296..000000000000 --- a/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=update_blastdb.pl for local blast db maintainance -EAPI=5 -HOMEPAGE=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux -LICENSE=public-domain -RDEPEND=dev-lang/perl !sci-biology/ncbi-tools++ -SLOT=0 -SRC_URI=ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/12_0_0/ncbi_cxx--12_0_0.tar.gz -_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f versionator 26ca8a8bd95d6a74122c08ba98a4ee72 -_md5_=bc882208706b78e231cbfd78c7b5799e diff --git a/metadata/md5-cache/sci-biology/vaal-46233-r2 b/metadata/md5-cache/sci-biology/vaal-46233-r2 deleted file mode 100644 index fb9109c2d202..000000000000 --- a/metadata/md5-cache/sci-biology/vaal-46233-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=!sci-biology/allpaths !sci-biology/allpathslg dev-libs/boost >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Algorithm for detecting SNPs, indels, and other polymorphisms -EAPI=6 -HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd/ -IUSE=openmp -KEYWORDS=amd64 -LICENSE=Whitehead-MIT -RDEPEND=!sci-biology/allpaths !sci-biology/allpathslg -SLOT=0 -SRC_URI=ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/vaal-46233.tar.gz ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc https://dev.gentoo.org/~mgorny/dist/vaal-46233_remove-namespace-std.patch.bz2 -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 -_md5_=7ca22b906d6f7e7c4fe2f2f35eedfb6b diff --git a/metadata/md5-cache/sci-biology/vcftools-0.1.14 b/metadata/md5-cache/sci-biology/vcftools-0.1.14 deleted file mode 100644 index 3fcd202d89bb..000000000000 --- a/metadata/md5-cache/sci-biology/vcftools-0.1.14 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 -DESCRIPTION=Tools for working with VCF (Variant Call Format) files -EAPI=6 -HOMEPAGE=http://vcftools.sourceforge.net/ -IUSE=lapack -KEYWORDS=~x86 ~amd64 -LICENSE=LGPL-3 -RDEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) -SLOT=0 -SRC_URI=https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz -_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=c40169dc993f3444a3e2f41ad69a920d diff --git a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 deleted file mode 100644 index b6c62a7e3240..000000000000 --- a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DEPEND=sys-libs/zlib doc? ( virtual/latex-base ) -DESCRIPTION=A sequence assembler for very short reads -EAPI=4 -HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ -IUSE=-doc -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib -SLOT=0 -SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=81d9bd82f6f3df3f4b73fa7d65b5d95e diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10 deleted file mode 100644 index a7028a35342b..000000000000 --- a/metadata/md5-cache/sci-biology/velvet-1.2.10 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install prepare test -DEPEND=doc? ( virtual/latex-base ) -DESCRIPTION=A sequence assembler for very short reads -EAPI=5 -HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ -IUSE=doc openmp -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz -_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=420632435bf1efe77241192fff993a20 diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 deleted file mode 100644 index 8a2b5ac3a1af..000000000000 --- a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install prepare test unpack -DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) python? ( dev-lang/swig:0 ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-lang/perl:=[-build(-)] -DESCRIPTION=RNA secondary structure prediction and comparison -EAPI=5 -HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/ -IUSE=doc openmp python static-libs python_targets_python2_7 -KEYWORDS=amd64 ppc x86 -LICENSE=vienna-rna -RDEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dev-lang/perl:=[-build(-)] -REQUIRED_USE=python? 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