diff options
Diffstat (limited to 'sci-biology')
35 files changed, 361 insertions, 798 deletions
diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild index 18a07a7b9f9f..1f5693d9a139 100644 --- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild +++ b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python3_6 ) +PYTHON_COMPAT=( python3_{6..9} ) inherit distutils-r1 @@ -12,9 +12,11 @@ HOMEPAGE="https://htseq.readthedocs.io/" if [[ ${PV} == *9999 ]]; then inherit git-r3 - EGIT_REPO_URI="https://github.com/simon-anders/htseq.git" + EGIT_REPO_URI="https://github.com/htseq/htseq.git" else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz" + + S="${WORKDIR}"/htseq-release_${PV} KEYWORDS="~amd64" fi @@ -25,7 +27,7 @@ RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND=" - ${RDEPEND} +DEPEND="${RDEPEND}" +BDEPEND=" >=dev-lang/swig-3.0.8 dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild index 18a07a7b9f9f..1f5693d9a139 100644 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ b/sci-biology/HTSeq/HTSeq-9999.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python3_6 ) +PYTHON_COMPAT=( python3_{6..9} ) inherit distutils-r1 @@ -12,9 +12,11 @@ HOMEPAGE="https://htseq.readthedocs.io/" if [[ ${PV} == *9999 ]]; then inherit git-r3 - EGIT_REPO_URI="https://github.com/simon-anders/htseq.git" + EGIT_REPO_URI="https://github.com/htseq/htseq.git" else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz" + + S="${WORKDIR}"/htseq-release_${PV} KEYWORDS="~amd64" fi @@ -25,7 +27,7 @@ RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND=" - ${RDEPEND} +DEPEND="${RDEPEND}" +BDEPEND=" >=dev-lang/swig-3.0.8 dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index 7112b7eebe07..e8c7f43fc23f 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1,4 +1,4 @@ -DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 -EBUILD HTSeq-0.9.1.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9 -EBUILD HTSeq-9999.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9 +DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64 +EBUILD HTSeq-0.12.4.ebuild 773 BLAKE2B 3e609a2928a83d5ba64900f44de659879950242466bd7df9973e1025b2b313c26c84a7d6457567b3188199c804586349ed61a56fcdd36c1bb99ab0cb459735b4 SHA512 53e6c0d43f1ed04e1b0ecd7a7d0844fdbb9ae8b6ec55c478b5b17ea42dd9067bb7571f36d33d1e4ea1b47560c6c383010679a72ecf8d759351c7651b49b68d04 +EBUILD HTSeq-9999.ebuild 773 BLAKE2B 3e609a2928a83d5ba64900f44de659879950242466bd7df9973e1025b2b313c26c84a7d6457567b3188199c804586349ed61a56fcdd36c1bb99ab0cb459735b4 SHA512 53e6c0d43f1ed04e1b0ecd7a7d0844fdbb9ae8b6ec55c478b5b17ea42dd9067bb7571f36d33d1e4ea1b47560c6c383010679a72ecf8d759351c7651b49b68d04 MISC metadata.xml 329 BLAKE2B f06dd42c6a1d3bca399cbe48d519346519b9acb0e4176ee79657e058ad1724b542242704e5cc3237873f338b1b23887715f95673957e533c057464ef07e8634f SHA512 04b82836732bf1415d6ce9d3b4c75139aa7d96382da2fd3343a54053172cffcac9ce96dab49b91852dea1a2a38b73cd90279c2c86496577bd6a79040a1fb6026 diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex dad4a363d8d0..fb1ebe38a141 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index c247c7af050a..2dc014f78dfe 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,9 +1,3 @@ -AUX bcftools-1.5-buildsystem.patch 376 BLAKE2B 384bf91c3af4f98c76c0ab6fecdfe0ec9483b77c54517df0ad2703441def7a7a6982ee792ae1775414ab8cec43d0e65ff6d2187be7cb85bb42eb5af8f9b7283e SHA512 c8ede2be5205ab287843662e7b97ecae8d4fc7d2aaf09e0b9fa67f5a3168149b15457e73c2c9d8b74fcfada08ec5c1bbe61013a2ef434ee50acf56eccabf6723 -AUX bcftools-1.5-fix-shebangs.patch 594 BLAKE2B 28d0a58627dcc1b1eb8f546c73a88f76e3277c82772f8a7af814d9ff3bcb116751b065166661c486e8c6b1708a54de227a5ef65d18a8527b38f5119d744539d2 SHA512 e00cc0de35ad5866f7321408a7995f054f80e37e642b6c3097c5e786635dc61baefa7ea8847f2222d32196825e3e44209d63fdfd219c54b09421a4bb310067f5 -AUX bcftools-1.9-buildsystem.patch 380 BLAKE2B b71567ad14d96b85bf449db473b38cd9ff2a32420d9c4d1b606cad0e09a478fd0946b589c62405aceacf234db7abde3fcf180eed7fbf0d8db73565b4424f86b8 SHA512 f0124734e6309eda73e5f32a9832e8c35de1929c6503627564346f097415bc76294371eda1886100ce2f1ed8e0de695e978a720dd4517e8411dcd041797af2b5 -AUX bcftools-1.9-fix-shebangs.patch 198 BLAKE2B 9d6c365c7193c7815216be4f8034c00e0048f7352e15ee24b4359828bf0906755ab9524fb10ad185754652b74007dc2c756b2260f64a263f696cf0f737ff25d7 SHA512 65eecc5e0d5cf3df1538b078c7606b38451e13f4f359ecf9287a9e03721c7c7ba1cd8bd517a98dd34842db22624fbdc570e9707d13f2e2fb82b16b3ca41ca71e -DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 -DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c -EBUILD bcftools-1.5.ebuild 868 BLAKE2B acfd6758e27cb9ade023d91074724affd0fa3016af565c809819fae615be61ca8af90edf6b38eaf0a4ed5f3e9eaaa19451096b8d7c27a58c6ed0540bf7260784 SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6 -EBUILD bcftools-1.9-r2.ebuild 1000 BLAKE2B eb5e7bb5f33f5ef22594eb241f3900ee6a6c125cb83b0e425732fbd6d781dac382b1664281e3256587ea8f344db578c1ec778ac2d5ae4794fa67931468cb580c SHA512 90d56585baae31be060fc8a54de5d86c1bd015da187d86a37ceee1176a685a864214e124770dfb895d568bb57e143f9a35b7f627f36598dbf4cb544119f2185d +DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300 +EBUILD bcftools-1.10.2.ebuild 870 BLAKE2B 2368cbe0d749a1214a8f1ad659bc3ea9b51b34c7c45b88e13d8c79eb6919ffcdd73a18e0a1119c5e92781cd79aa184360a9b0fd4187beebaed66ac89d934396f SHA512 9888597c6bd9412688c8375962e9f8a1c4722ca905f57b1d7c729e433ee353b3956fddf397fe65f0f8523f8e588062f02267ec9024bf6c8c3858cd9fa183916a MISC metadata.xml 343 BLAKE2B e1664c6d67ebde81b9f99b69d442e0b16891ecd392fddd55ed2aaa885dcb2f4ca39cd627cd3f6367f39b13e35eb1141119e53756d6efc4ac62c819ab1d611633 SHA512 cfa167a5733f40d7e36e9e229229acd883ba7bfd812afb9060c742c505354b1c754070e2e897a48d7611a123b9606b6f43a0816c089e71bf64f3d0dbd8b7184d diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild b/sci-biology/bcftools/bcftools-1.10.2.ebuild index 0963c692fcd6..179f7dea77e4 100644 --- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild +++ b/sci-biology/bcftools/bcftools-1.10.2.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python3_{6,7} ) +PYTHON_COMPAT=( python3_{6..9} ) inherit python-single-r1 @@ -26,11 +26,6 @@ RDEPEND=" ${PYTHON_DEPS}" DEPEND="${RDEPEND}" -PATCHES=( - "${FILESDIR}"/${PN}-1.9-buildsystem.patch - "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch -) - src_prepare() { default @@ -44,6 +39,5 @@ src_configure() { econf \ --disable-bcftools-plugins \ --disable-libgsl \ - --disable-configure-htslib \ --with-htslib=system } diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild deleted file mode 100644 index 9b5df1130999..000000000000 --- a/sci-biology/bcftools/bcftools-1.5.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org" -SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}*:= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.5-buildsystem.patch - "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch -) - -src_prepare() { - default - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --disable-bcftools-plugins \ - --disable-libgsl \ - --disable-configure-htslib \ - --with-htslib=system -} diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch deleted file mode 100644 index 304fc03e7441..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -275,7 +275,6 @@ - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) - - clean: testclean clean-plugins - -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch deleted file mode 100644 index c6cfc8b991d3..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- a/misc/guess-ploidy.py -+++ b/misc/guess-ploidy.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2.7 - # - # Plot the output of "bcftools +guess-ploidy -v" - # ---- a/misc/plot-roh.py -+++ b/misc/plot-roh.py -@@ -1,4 +1,4 @@ --#!/usr/bin/python -+#!/usr/bin/env python2.7 - - import glob, gzip, csv, sys, os, copy, re - csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch deleted file mode 100644 index a0df4b917bcb..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -282,7 +282,6 @@ - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) - - clean: testclean clean-plugins - -rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch deleted file mode 100644 index 76610187c493..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 8d91db427f4f..5258bcd3f805 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,4 +1,6 @@ -DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 -DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def -EBUILD bedtools-2.26.0.ebuild 959 BLAKE2B c3d42f033913e18a9bd1f0b6f669a4000bc6b6892bbd5986a33a99ed496ae4af11b690f1c7c350644b62e77baef80a9eb52f15e87818a74b684d4fac816a2512 SHA512 a3914d04806fa4b3f14f83d91717d00fd183e1f6d4a39690ae04e7767791605a8e90d86cefc4deaa50327651c64125808658de4471f05df936c19e46768bf988 +AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85 +AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f +AUX bedtools-2.29.2-samtools-1.10.patch 659 BLAKE2B 5ec159e0a9bc9f4b5d661bcf93ba8a0cd08f62e8e6d3f92229b71d5dfb122d89eb6a68637e12394e6082cf9be99014787f9a780f7fb547ec61f5f8b8d405713d SHA512 0160c54ad3781e17df53b2525cbf0e6b5d1ebf5ce07257b16c35eed525623aa46b5ee32f158ab64b2e18a283eba0f8331a521ac8382cc31ca03cd88d1376c057 +DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5 +EBUILD bedtools-2.29.2.ebuild 1232 BLAKE2B 6e5204cbdae38787b2667fd383ee2c5f8dcd2f08569b2454280bfc1e8821dafe46dce4eb4ed4b3f55b22c19dea5705fea25816f93b449feea3163dac6667dbc5 SHA512 ba09db688e841fa10d65e19534b6c0d903352f5a04996bd451df5ada09f8379b6a0b8bdbbdedd7b5ecda51036bc6c37bc512dd9a4c321ade4fdca10f30407474 MISC metadata.xml 406 BLAKE2B 5a16830031644c5087241b9e20afcb6315095c877e2b019eace76ee0602929c168c2273e27e99f03ca3c1a57db0bf728c2d8ccc39b7f80588bb215d1fd6a3ea6 SHA512 35a9b50a772503e6691faf1e2f1093bd6ffd5f6f5be08b1ad8581948f4f3e8fb7e54faa101cff757fc561ed71696253114c32fb6293df59cda3e8fd7c24d2bb0 diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild deleted file mode 100644 index b062a6fef84d..000000000000 --- a/sci-biology/bedtools/bedtools-2.26.0.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -inherit flag-o-matic python-any-r1 toolchain-funcs - -DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" -HOMEPAGE="https://bedtools.readthedocs.io/" -SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz - https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="${PYTHON_DEPS} - test? ( - sci-libs/htslib - sci-biology/samtools:0 - )" -RDEPEND="sys-libs/zlib" - -S="${WORKDIR}/${PN}2" - -DOCS=( README.md RELEASE_HISTORY ) -PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) - -src_configure() { - append-lfs-flags - export prefix="${EPREFIX}/usr" - tc-export AR CXX -} - -src_install() { - default - - insinto /usr/share/${PN} - doins -r genomes -} diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild new file mode 100644 index 000000000000..fbc1f3a9b4f9 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6..9} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +S="${WORKDIR}"/${PN}2 + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch + "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch new file mode 100644 index 000000000000..573e88993bc9 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch @@ -0,0 +1,82 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,44 +4,29 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := bash -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt + + + # define our object and binary directories +-ifeq ($(VERBOSE),1) + CCPREFIX = +-else +-CCPREFIX = @ +-endif + + OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ +- +-ifeq ($(DEBUG),1) +-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0 +-else + BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -g -Wall -O2 +-endif ++BT_CXXFLAGS = -Wall + + # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). +-ifeq ($(USE_RAND),1) +-BT_CXXFLAGS += -DUSE_RAND +-else + BT_CXXFLAGS += -std=c++11 +-endif + + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++prefix = $(EPREFIX)/usr + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -204,7 +189,7 @@ + + # make the "obj/" and "bin/" directories, if they don't exist + $(OBJ_DIR) $(BIN_DIR): +- @mkdir -p $@ ++ mkdir -p $@ + + + # Usually HTSlib's configure script has not been used (detected via config.mk +--- a/src/utils/htslib/Makefile ++++ b/src/utils/htslib/Makefile +@@ -22,20 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib +- + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = + LIBS = $(htslib_default_libs) + + prefix = /usr/local diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch new file mode 100644 index 000000000000..9576a78bd1dd --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch @@ -0,0 +1,41 @@ +--- a/Makefile ++++ b/Makefile +@@ -183,7 +168,7 @@ + + $(BIN_DIR)/intersectBed: | $(BIN_DIR) + @echo "- Creating executables for old CLI." +- @python scripts/makeBashScripts.py ++ $(EPYTHON) scripts/makeBashScripts.py + @chmod +x bin/* + @echo "done." + +--- a/src/utils/BamTools/Makefile.frag ++++ b/src/utils/BamTools/Makefile.frag +@@ -1,4 +1,4 @@ + src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map + + src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map +- python $^ > $@ ++ $(EPYTHON) $^ > $@ +--- a/test/bigchroms/test-bigchroms.sh ++++ b/test/bigchroms/test-bigchroms.sh +@@ -28,7 +28,7 @@ + rm obs + + if [[ "$BT_NO_BIG_FILES" != "" ]]; then +-python make-big-chrom.py ++${EPYTHON} make-big-chrom.py + + echo -e " bigchroms.t03...big get fasta \c" + $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs +--- a/test/fisher/cmp.sh ++++ b/test/fisher/cmp.sh +@@ -3,7 +3,7 @@ + echo "fisher,shuffled" + + for i in $(seq 1000); do +- fisher=$(python ./sim.py | tail -1 | cut -f 2) ++ fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2) + shuffle=$(bash shuf.sh) + echo "$fisher,$shuffle" + done diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch new file mode 100644 index 000000000000..7cc0e23de2d4 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch @@ -0,0 +1,13 @@ +--- a/test/intersect/new_test-intersect.sh ++++ b/test/intersect/new_test-intersect.sh +@@ -975,8 +975,8 @@ + # Test intersect preserve the text header in bam + ############################################################ + echo -e " intersect.new.t78...\c" +-echo -e "@HD VN:1.5 SO:coordinate" > exp +-echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs ++echo -e "@HD VN:1.5 SO:coordinate" > exp ++echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs + check exp obs + rm exp obs + [[ $FAILURES -eq 0 ]] || exit 1; diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest index bc34d9deef95..9504afbb1e06 100644 --- a/sci-biology/biopandas/Manifest +++ b/sci-biology/biopandas/Manifest @@ -1,3 +1,3 @@ -DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8 -EBUILD biopandas-0.2.1.ebuild 1074 BLAKE2B df4d27cdd692e603cb70889c9ce17768a76de67b1c92d5fa9b9c6df4e2ac1973f5e35f8bdee85b4eeac9b706fe0729cba28e868c460cf3f6ca43363c51131aee SHA512 af744459bcf4460c2303b78064f3855041efd3a03b26f8a60cca844e6fdc7eb2bb39c22d981e464a4357c15787aed2f0cda58afe3604bcc96e0d11303e0e4306 +DIST biopandas-0.2.7.tar.gz 255846 BLAKE2B b8c6a66f51a00266bc1a271ecfe00b4cfddd24b9766e63e2ad4187048ddd8f985d70eb8083b1be3887a0fd9b666c97553029ecd90c7b73ae882e5347bbc54d2e SHA512 cf4f12601b7f63ca3d5e9a17c6628e4975968f722c9db72e32c00e80ec335c5bf6a928a5f887b16ecd316c49b298d77634cbe1c4ef1ca505379b1de5335e2569 +EBUILD biopandas-0.2.7.ebuild 1027 BLAKE2B ffea926f1e452998df12ecef094f69e7100bb4c1a8e32dd444e9ae605023d651dba05f148e004d7ffa367e7434c5dec5fb35dec5c379ead9cb9cac6d10948f1c SHA512 d77e77c37353e71fbd8094984ac75d5c21b6bd6ca09fa8146648f388eb352240f78f80b7f23c82b9ff4295c2a84452f902dc5cfc1ddcaaba8a1d3ad6a4fd8de8 MISC metadata.xml 536 BLAKE2B e3cb776d0332fff486a7e1ea1353c54694ff687d4685bbb51728db0ed2025bb3d09d39cf7c9ea9f11546cbf9c4727661348e2f5fdfc13ffac2329ef6dfbe7450 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166 diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.7.ebuild index 8c892419b29c..9be9a8ac4a3c 100644 --- a/sci-biology/biopandas/biopandas-0.2.1.ebuild +++ b/sci-biology/biopandas/biopandas-0.2.7.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python3_6 ) +PYTHON_COMPAT=( python3_{6..9} ) inherit distutils-r1 @@ -26,18 +26,15 @@ RESTRICT="!test? ( test )" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/nose[${PYTHON_USEDEP}] - )" + sci-libs/scipy[${PYTHON_USEDEP}]" + +distutils_enable_tests nose python_test() { - "${EPYTHON}" --version - "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" - "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" - "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" + "${EPYTHON}" --version || die + "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" || die + "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" || die + "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" || die + nosetests -s --verbose ${PN} || die } diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index f252db4b4e14..0141c7450dbb 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1,3 @@ -DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f -EBUILD biopython-1.73.ebuild 1671 BLAKE2B d899d54d6983bbbcc43e34a051cd5cfdbed4ff92d50dcc95fd38df84f60882bfdda7d95cf4a5fa84ece32e36e10e53010340cdceb2f50b37351b917afd0dc062 SHA512 3d648fe4b0a62f984fe4541c8b4298759dcf772ef0119ca7de42b207fc09994ed2c5d0b3a561fc647382c2e41f2ec1832fe388c7fdf1f8b8d83ee4565d0e20b1 +DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5 +EBUILD biopython-1.77.ebuild 1855 BLAKE2B 739e5cc4a954ac9cc5fe0640ac5f418ad1ee1aadb66570a41996e8e260dc75c8c4373c94b53b0d147d1b661169c1aa3352b9367ab0e37cfd8bd05c220186ac92 SHA512 e2dd1ef79804c779645162410e6890d0618d080ac20195cae0097fe3a42c204d270321949e8d5056b85f9e9a5ed598e05c20f2869178dd16ea86ea105167271a MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.77.ebuild index 94acdfc2a2cb..486e9fe694d1 100644 --- a/sci-biology/biopython/biopython-1.73.ebuild +++ b/sci-biology/biopython/biopython-1.77.ebuild @@ -3,7 +3,8 @@ EAPI=7 -PYTHON_COMPAT=( python3_{6,7} ) +PYTHON_COMPAT=( python3_{6..9} ) + inherit distutils-r1 eutils DESCRIPTION="Python modules for computational molecular biology" @@ -13,7 +14,6 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="HPND" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] @@ -23,15 +23,20 @@ RDEPEND=" dev-python/pygraphviz[${PYTHON_USEDEP}] >=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}] dev-python/pydot[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - sys-devel/flex" +DEPEND="${RDEPEND}" +BDEPEND="sys-devel/flex" DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. ) python_test() { distutils_install_for_testing - cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die + cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die + + # need to create symlinks for doctests + mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die + ln -r -s "${S}"/Bio/Align/substitution_matrices/data \ + "${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die + cd "${TEST_DIR}"/lib/Tests || die rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die "${EPYTHON}" run_tests.py --offline --verbose || die diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest index 7a4e2f33be3e..b4ae775226b6 100644 --- a/sci-biology/blat/Manifest +++ b/sci-biology/blat/Manifest @@ -1,4 +1,5 @@ AUX blat-34-fix-build-system.patch 5249 BLAKE2B d32fcb326cd204c847a678cabd3fc666ed9285876ec4a3f3dc1873b9b8c83042eb705cf62e63d00b6f388540571d4ebadc497eef51827a30443d3a2aebed9420 SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246 +AUX blat-34-fno-common.patch 466 BLAKE2B 51dd1778f09e51ce1e345ae9474d3aaeb8535b739bc6d46e5d9271204b7043e1c5da0865ed3392b62d85b75c4d6c6611015042d359a113a9b0540c9ae1f6e448 SHA512 fa0b327f212137afa41d8d21717b02c77cf7e8228fe6b104af4a9a430fb0ed11a49be1ae38e8b51016ed5b6c43073c6cbbf27cd8b6f8396d39e623039d700abf DIST blatSrc34.zip 2142975 BLAKE2B 88a2da3b1551d5d50aaa507978c17cbe34de5a27efee9405829aea51b0950b748775f21e8d806470ba5ee7831fe71d6d87cd126c38727f25306a0f793543912e SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8 -EBUILD blat-34-r2.ebuild 807 BLAKE2B 03979dd5b1b320c8560a8d9a50c6484fc052fadfd5e7d4cb80f3ac7a769f99b3da20fb42192087cd5652d947385de32ec9649c4d33b6f2c0430bfb5b14e9ce63 SHA512 451b189b505331cd7c045fc19982d55d11673afdfa8f0f9bd2b57cd23097c5a066afe477d973a0f30e1a47a8d1893abc552ef8ccc5f59ce9f3a66e0ceedc94b2 +EBUILD blat-34-r2.ebuild 841 BLAKE2B b85ced6d272519445d60bb5846a6fa135a214aaa4b5ffed12f77b5beef8be5f3f48ffe0e4835ecc8cbf937f233c0d18a15a7168149d31fb5d2eea508ac915431 SHA512 3b34227db3d38640ba5affe00c43c0512091e007dc21625310c169e9f44a412d47039160d952c873c0afb6f5b062e1186ea5eaacf71086093807b3169ba7b956 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild index e10bc367a311..b07246356381 100644 --- a/sci-biology/blat/blat-34-r2.ebuild +++ b/sci-biology/blat/blat-34-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -21,7 +21,10 @@ DEPEND="app-arch/unzip" S=${WORKDIR}/${MY_PN} -PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-34-fix-build-system.patch + "${FILESDIR}"/${PN}-34-fno-common.patch +) src_compile() { tc-export AR CC diff --git a/sci-biology/blat/files/blat-34-fno-common.patch b/sci-biology/blat/files/blat-34-fno-common.patch new file mode 100644 index 000000000000..63a49cf81299 --- /dev/null +++ b/sci-biology/blat/files/blat-34-fno-common.patch @@ -0,0 +1,11 @@ +--- a/inc/htmshell.h ++++ b/inc/htmshell.h +@@ -85,7 +85,7 @@ void htmlBadVar(char *varName); + void htmlImage(char *fileName, int width, int height); + /* Display centered image file. */ + +-jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */ ++extern jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */ + + void htmlVaWarn(char *format, va_list args); + /* Write an error message. (Generally you just call warn() or errAbort(). diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest index 30219f3ec6ee..70b96c98971e 100644 --- a/sci-biology/clustalw/Manifest +++ b/sci-biology/clustalw/Manifest @@ -2,5 +2,5 @@ AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0 DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a EBUILD clustalw-1.83-r4.ebuild 815 BLAKE2B 9a887de5a2a1e96652d260963e13c9aca786b684ee2a9b0c02adba0b2fbfcf0f500f5edabaf4469b2e5ff13b3cf445245d59010b5f8a50e9d830d636f0f76699 SHA512 c884a8fb3029e7834299217c6db91da4f3430c738ba346dc7c3431695c235852c830151452ec534f1c1e59aaff5fbd4bb2d1030ed7779f30a675cbb30d76c218 -EBUILD clustalw-2.1-r1.ebuild 473 BLAKE2B 76c7432b4cd6d68b5dd51bdc9b4e1629d8e958f432bb9c35738373bc7ea34180e74c9d0ba498d02e5d4db3243ccd711255157490d4b42d84bc7b0b493f526234 SHA512 6cd64a7ffa784daeef1146a695e588a78e74b5b453e3cc1751907fbe09aa394eb9c962e681ecdef9eb2627d5c490a49ff58484c2c77599f169d48482521749e0 +EBUILD clustalw-2.1-r1.ebuild 489 BLAKE2B af8ab15dcb6e2fb20199c7054940eaf53bbbcc72ec1fd7c37fc0aa3f3c28e7a23c640e70eb33956367a12ecc04990a3d6b63ad2b3d8bdf35396debff35dc6da6 SHA512 ad9b200b16d55df114440a44f8d771a406e518a49ca140de106ee38b4e8afc7f0acc7ccb18d81ea90f541637013915c6e793832d26a8b4465925fa101747498c MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild index 0b46aeb5bfd4..f42f1ed031b0 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="" src_install() { diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 7f96ff719811..b61c521c5275 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,4 +1,4 @@ -AUX pysam-0.12-fix-buildsystem.patch 2356 BLAKE2B 95542f99b411a00eeaa24836cb7489bf2bbf690d804669f69f6f1a8c07f66d9c6ef34624eb511036cd36b1268b49959d38db497cb557e9cc40f3a35b2d349f4d SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a -DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d -EBUILD pysam-0.12.0.1.ebuild 1182 BLAKE2B 11c3a036ca7c6560a6316963ea6133708d36cce2d0f21a1e327180d303406ae23ad021ba04024191eda1687ef538f41c0bfe34bbed742bc85f9aeb12b38dc6da SHA512 fd71cf196e68f640343e2b43e3bb8b5355462f6816a1eb0e7755d188435c567ce53209f6f2599a84e5052d26b4747038c7a4b5a2e9b916c117f388ca369a3919 +AUX pysam-0.16.0.1-fix-tests.patch 1128 BLAKE2B 8e395496c23186b29622b8e87369f910326724b70b63f3eccfd6d4b6cea86abf8b34a712a931f205711e2c5a6e76c9572a93aa9bd994f915312c55dcc888da52 SHA512 e725143c72d04fc0e2e37e607e6d9b85b4c883bcc5a530ff3c92e3bbd45d7d7fb09c315766a19254bea2a19a2d00a5f64220094a4e9b1090e412b26ea489b530 +DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28 +EBUILD pysam-0.16.0.1.ebuild 1393 BLAKE2B a124ddf7b18e31a89d3fe0d47c7f938d5edfe65938bf0360de209cfa7545474f4be780b7a9e8b4c73fa4cd9282ac9176d8289a34805e062176dbacf3405f33d7 SHA512 b24b2c7d9d764a2e451f4f1c00a20ccc203079e17c238f909b5afb5c6d0a26303822ef54920209f22bf9ba08b3a8a27ff7c052d8bf571a14baca511524a28cdc MISC metadata.xml 410 BLAKE2B ed86e3ffe38a306e581762625b37cf6596dc2a2ba404406ab12f681d5b48529764e281d40411bedbdf6016bc57d02adb705e8c8703b8120cf89b4961f75bed67 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810 diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch deleted file mode 100644 index 8b323a63fba5..000000000000 --- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch +++ /dev/null @@ -1,63 +0,0 @@ -The build system is not designed with partial out-of-source -builds in mind. This is evident by using relative includes -such as '-Isamtools' instead of proper relative or absolute -paths. - -Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 - ---- a/setup.py -+++ b/setup.py -@@ -359,6 +359,8 @@ - - define_macros = [] - -+samtools_include_dirs = [os.path.abspath("samtools")] -+ - chtslib = Extension( - "pysam.libchtslib", - [source_pattern % "htslib", -@@ -385,7 +387,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, -+ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -404,7 +406,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs, -+ include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -423,7 +425,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, -+ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -467,7 +469,7 @@ - htslib_sources + - os_c_files, - library_dirs=["pysam"] + htslib_library_dirs, -- include_dirs=["samtools", "pysam", "."] + -+ include_dirs=["pysam", "."] + samtools_include_dirs + - include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", -@@ -482,7 +484,7 @@ - htslib_sources + - os_c_files, - library_dirs=["pysam"] + htslib_library_dirs, -- include_dirs=["bcftools", "pysam", "."] + -+ include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs + - include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch new file mode 100644 index 000000000000..9d269878e651 --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch @@ -0,0 +1,37 @@ +--- a/tests/pysam_data/Makefile ++++ b/tests/pysam_data/Makefile +@@ -3,7 +3,7 @@ + BAI=$(BAM:%.bam=%.bam.bai) + CRAM=ex1.cram ex2.cram ex3.cram + CRAI=$(CRAM:%.cram=%.cram.crai) +-NO_PG:=$(findstring --no-PG,$(shell samtools view)) ++NO_PG:=--no-PG + + # ex2.bam - bam file without index + +--- a/tests/tabix_test.py ++++ b/tests/tabix_test.py +@@ -14,6 +14,7 @@ + import subprocess + import glob + import re ++import pytest + from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \ + load_and_convert, TABIX_DATADIR, get_temp_filename + +@@ -1014,6 +1015,7 @@ + globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,)) + + ++@pytest.mark.skip(reason="requires internet connectivity") + class TestRemoteFileHTTP(unittest.TestCase): + + url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" +@@ -1053,6 +1055,7 @@ + self.assertEqual(list(self.local_file.header), []) + + ++@pytest.mark.skip(reason="requires internet connectivity") + class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP): + + url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz" diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.16.0.1.ebuild index e7567f3501bf..acc0cb99892f 100644 --- a/sci-biology/pysam/pysam-0.12.0.1.ebuild +++ b/sci-biology/pysam/pysam-0.16.0.1.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python3_6 ) +PYTHON_COMPAT=( python3_{6..9} ) inherit distutils-r1 @@ -11,18 +11,25 @@ DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping for HOMEPAGE=" https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="=sci-libs/htslib-1.5*:=" +RDEPEND="=sci-libs/htslib-1.10*:=" DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.10* + =sci-biology/samtools-1.10* + )" -PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 python_prepare_all() { # unbundle htslib @@ -31,17 +38,23 @@ python_prepare_all() { export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) rm -r htslib || die - # prevent setup.py from adding RPATHs - sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ - -i cy_build.py || die + # prevent setup.py from adding RPATHs (except $ORIGIN) sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ -i setup.py || die + eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + distutils-r1_python_prepare_all } -src_compile() { - # TODO - # empty compile, as the build system runs the whole build again in install - : +python_compile() { + # breaks with parallel build + local MAKEOPTS=-j1 + distutils-r1_python_compile } diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 45ef440561f3..0c9eb58c3dc7 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,9 +1,6 @@ AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d -AUX samtools-1.5-buildsystem.patch 18442 BLAKE2B df389fd2eb6cfa4fafc987eb8e2e1e5d050a9373305f752516c77f415619f5c5b7ff8e2f8c8fd04769c269f9d385f0130443311d9468a591a4531a9e3127725f SHA512 2405c9c5bd2892756dd70147d0bc57f11f869ac2b6bb12d4350e3f7145727a4c8a602489bca5dbcbe8131d52572d4573e8507a2b989ac0ac86aa8dfef92e58d4 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 -DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 -DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f -EBUILD samtools-0.1.20-r3.ebuild 2363 BLAKE2B 6050d698f26b9962192cdbc6c3729bb812041fc92f4ba4490dc6f50e71c08853d6e2e4c6592c324c3efc3ac0da058e8b254475d6fc788f314798cdcaf85a4fc0 SHA512 f79e0f723d86e7c2060163a3b79e6624ea58d21e7c8ddeb87be40a7972cd97e60df82dacaae23b8a89cec2a0517ffdae8804ac71044685b40d5c5769f8964557 -EBUILD samtools-1.5.ebuild 1107 BLAKE2B 2088a3fcc483de227bd92c80cd9ae2bf0257af773298bebcd077d7b2385eb43a6bfde82c7fadb0e2af3400b825e5b1b3c3c4f633cc7631beb4d0dcbb39cdd2cf SHA512 2f1701695fe3aa270bd75bedc3f847b3057ea1a6d9dca386a8f420df22ab78f51b12c8e1ca80d7d2fb1221d246047a78e914022c8e4c8bae5b0b053f3b130cfd -EBUILD samtools-1.9-r1.ebuild 926 BLAKE2B a71ab1165f9fad65f0ff932880a661fb43435ebc1c72839ed8f57d3a1ee8b11d5441d53404ed650d634334a8f197d4275f82831d7332bdbbe6f110506f0d0230 SHA512 f75851ece84f8863c7352fad6133fe66299cfe94561a62f7dd4a2bf9a82d2a2400be483874d109b67b643807a25d6907d47c8310732d4b13577e27af685857bd +DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a +EBUILD samtools-0.1.20-r4.ebuild 2040 BLAKE2B d90fc78a99b4134ba1a277ceb904c65592f1d29222822f5c97e31a46cbc4138af6adc763c7b05cf26bc0de06ac23ca0b8d8891841ecfd6c1b3fafd270e24216d SHA512 855e19ca8d0dcb9d472398895c666324d00355a7b04c075744e7ac58be1d183f7739f9a254c5bbdaf4171ab6324159860be40171693d0f2f5074884b9eba5e87 +EBUILD samtools-1.10.ebuild 991 BLAKE2B 206a77657bc9a82d6a7536d030b726a0450bbba406e4e7ec9cc670ee530b87d871111952c850d4008c436f81d3daeba802eb4a3442b59ff9ab0f5864bc4fcf21 SHA512 efb1f235e3e3996599df79317e9c7c2ca5434b666a93f91c495550ac4846905e99d96dd1a6876d22a489b684bf24a90c6f6afb4cec5677c5c45f28f0c4f35b35 MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch deleted file mode 100644 index c466e66a9d17..000000000000 --- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch +++ /dev/null @@ -1,413 +0,0 @@ ---- a/config.mk.in -+++ b/config.mk.in -@@ -28,27 +28,26 @@ - # in the Makefile to reflect your configuration choices. If you don't run - # configure, the main Makefile contains suitable conservative defaults. - --prefix = @prefix@ --exec_prefix = @exec_prefix@ --bindir = @bindir@ --datarootdir = @datarootdir@ --mandir = @mandir@ -+prefix = @prefix@ -+exec_prefix = @exec_prefix@ -+bindir = @bindir@ -+libdir = @libdir@ -+datarootdir = @datarootdir@ -+mandir = @mandir@ -+man1dir = $(mandir)/man1 - - CC = @CC@ -+AR = @AR@ - CPPFLAGS = @CPPFLAGS@ - CFLAGS = @CFLAGS@ - LDFLAGS = @LDFLAGS@ - LIBS = @LIBS@ - --@Hsource@HTSDIR = @HTSDIR@ --@Hsource@include $(HTSDIR)/htslib.mk --@Hsource@include $(HTSDIR)/htslib_static.mk --@Hsource@HTSLIB = $(HTSDIR)/libhts.a --@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS) --@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) --@Hsource@BGZIP = $(HTSDIR)/bgzip --HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ --@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ --@Hinstall@HTSLIB_LIB = -lhts -+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@ -+HTSLIB_LIBS = @HTSLIB_LIBS@ - --CURSES_LIB = @CURSES_LIB@ -+NCURSES_CFLAGS = @NCURSES_CFLAGS@ -+NCURSES_LIBS = @NCURSES_LIBS@ -+ -+ZLIB_CFLAGS = @ZLIB_CFLAGS@ -+ZLIB_LIBS = @ZLIB_LIBS@ ---- a/configure.ac -+++ b/configure.ac -@@ -29,9 +29,6 @@ - AC_CONFIG_SRCDIR([bamtk.c]) - AC_CONFIG_HEADERS([config.h]) - --m4_include([m4/ax_with_curses.m4]) --m4_include([m4/ax_with_htslib.m4]) -- - dnl Copyright notice to be copied into the generated configure script - AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. - -@@ -39,73 +36,27 @@ - redistribute it. There is NO WARRANTY, to the extent permitted by law.]) - - AC_PROG_CC -+AM_PROG_AR - - AC_SYS_LARGEFILE - --AX_WITH_HTSLIB --if test "$ax_cv_htslib" != yes; then -- AC_MSG_ERROR([HTSlib development files not found -- --Samtools uses HTSlib to parse bioinformatics file formats etc. Building it --requires an unpacked HTSlib source tree (which will be built in conjunction --with samtools) or a previously-installed HTSlib. In either case you may --need to configure --with-htslib=DIR to locate the appropriate HTSlib. -- --FAILED. You must supply an HTSlib in order to build samtools successfully.]) --fi -- --if test "$ax_cv_htslib_which" = source; then -- Hsource= -- Hinstall='#' --else -- Hsource='#' -- Hinstall= --fi --AC_SUBST([Hsource]) --AC_SUBST([Hinstall]) -+dnl htslib -+PKG_CHECK_MODULES([HTSLIB], [htslib]) - -+dnl ncurses - AC_ARG_WITH([curses], - [AS_HELP_STRING([--without-curses], - [omit curses support, so no curses library needed])]) - --if test "$with_curses" != no; then -- AX_WITH_CURSES -- if test "$ax_cv_curses" != yes; then -- AC_MSG_ERROR([curses development files not found -- --The 'samtools tview' command uses the curses text user interface library. --Building samtools with tview requires curses/ncurses/etc development files --to be installed on the build machine; you may need to ensure a package such --as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based --Linux distributions) is installed. -- --FAILED. Either configure --without-curses or resolve this error to build --samtools successfully.]) -- fi --else -- CURSES_LIB= -- CURSES_CPPFLAGS= -- AC_SUBST([CURSES_LIB]) -- AC_SUBST([CURSES_CPPFLAGS]) --fi -- --save_LIBS=$LIBS --zlib_devel=ok --dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests --AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) --AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) --LIBS=$save_LIBS -- --if test $zlib_devel != ok; then -- AC_MSG_ERROR([zlib development files not found -- --Samtools uses compression routines from the zlib library <http://zlib.net>. --Building samtools requires zlib development files to be installed on the build --machine; you may need to ensure a package such as zlib1g-dev (on Debian or --Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. -+AS_IF([test "x$with_curses" != "xno"], [ -+ PKG_CHECK_MODULES([NCURSES], [ncurses]) -+ -+ AC_DEFINE([HAVE_CURSES], [1]) -+ AC_DEFINE([HAVE_NCURSES_H], [1]) -+]) - --FAILED. This error must be resolved in order to build samtools successfully.]) --fi -+dnl zlib -+PKG_CHECK_MODULES([ZLIB], [zlib]) - - AC_CONFIG_FILES([config.mk]) - AC_OUTPUT ---- a/Makefile -+++ b/Makefile -@@ -21,14 +21,6 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --AR = ar --CPPFLAGS = --#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 --CFLAGS = -g -Wall -O2 --LDFLAGS = --LIBS = -- - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o - AOBJS= bam_index.o bam_plcmd.o sam_view.o \ -@@ -40,13 +32,6 @@ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - --prefix = /usr/local --exec_prefix = $(prefix) --bindir = $(exec_prefix)/bin --datarootdir = $(prefix)/share --mandir = $(datarootdir)/man --man1dir = $(mandir)/man1 -- - # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) - misc_bindir = $(bindir) - -@@ -85,15 +70,14 @@ - - all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS) - --ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) --ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(LIBS) -+ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS) -+ALL_LIBS = $(ZLIB_LIBS) $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - - config.mk: -- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ -+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ -@@ -133,17 +117,22 @@ - .c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $< -+ - - LIBST_OBJS = sam_opts.o sam_utils.o - - --lib:libbam.a -+lib: libbam.so.1.0 - --libbam.a:$(LOBJS) -- $(AR) -csru $@ $(LOBJS) -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -+ ln -sf $@ libbam.so.1 -+ ln -sf $@ libbam.so - --samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread -+samtools: $(AOBJS) libbam.so.1.0 libst.a -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread - - # For building samtools and its test suite only: NOT to be installed. - libst.a: $(LIBST_OBJS) -@@ -151,58 +140,58 @@ - $(AR) -rcs $@ $(LIBST_OBJS) - - --bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) --bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) --bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) --bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) --bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) --sam_h = sam.h $(htslib_sam_h) $(bam_h) --sam_opts_h = sam_opts.h $(htslib_hts_h) --sample_h = sample.h $(htslib_kstring_h) -- --bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h --bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) --bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h) --bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h) --bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -+bam_h = bam.h -+bam2bcf_h = bam2bcf.h -+bam_lpileup_h = bam_lpileup.h -+bam_plbuf_h = bam_plbuf.h -+bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h) -+sam_h = sam.h $(bam_h) -+sam_opts_h = sam_opts.h -+sample_h = sample.h -+ -+bam.o: bam.c config.h $(bam_h) sam_header.h -+bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h) -+bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h) -+bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h) -+bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h) - bam_aux.o: bam_aux.c config.h $(bam_h) --bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h -+bam_cat.o: bam_cat.c config.h samtools.h - bam_color.o: bam_color.c config.h $(bam_h) --bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) --bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h --bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) --bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h --bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h --bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) --bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) --bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h --bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) --bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h --bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h --bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h --bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h --bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) -+bam_import.o: bam_import.c config.h $(bam_h) -+bam_index.o: bam_index.c config.h samtools.h -+bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) -+bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h -+bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h -+bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h) -+bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -+bam_quickcheck.o: bam_quickcheck.c config.h -+bam_reheader.o: bam_reheader.c config.h samtools.h -+bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h) -+bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h -+bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h -+bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h -+bam_stat.o: bam_stat.c config.h samtools.h -+bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h) - bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) - bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h) --bam_flags.o: bam_flags.c config.h $(htslib_sam_h) --bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) --bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h --bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) --bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) --cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h) --dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h) --faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h --padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h --phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) --sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h) -+bam_flags.o: bam_flags.c config.h -+bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h) -+bamtk.o: bamtk.c config.h samtools.h version.h -+bedcov.o: bedcov.c config.h $(sam_opts_h) -+bedidx.o: bedidx.c config.h -+cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h) -+dict.o: dict.c config.h -+faidx.o: faidx.c config.h samtools.h -+padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h -+phase.o: phase.c config.h $(sam_opts_h) samtools.h -+sam.o: sam.c config.h $(sam_h) -+sam_header.o: sam_header.c config.h sam_header.h - sam_opts.o: sam_opts.c config.h $(sam_opts_h) - sam_utils.o: sam_utils.c config.h samtools.h --sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) --sample.o: sample.c config.h $(sample_h) $(htslib_khash_h) --stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h) --stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) -+sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h) -+sample.o: sample.c config.h $(sample_h) -+stats_isize.o: stats_isize.c config.h stats_isize.h -+stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h) - - - # test programs -@@ -224,30 +213,30 @@ - - - test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - --test_test_h = test/test.h $(htslib_sam_h) -+test_test_h = test/test.h - - test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h) - test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o -@@ -256,34 +245,34 @@ - test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h) - test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h) - test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h) --test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h) --test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h) -+test/test.o: test/test.c config.h $(test_test_h) -+test/vcf-miniview.o: test/vcf-miniview.c config.h - - - # misc programs - - misc/ace2sam: misc/ace2sam.o -- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - - misc/maq2sam-short: misc/maq2sam-short.o -- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - - misc/maq2sam-long: misc/maq2sam-long.o -- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - - misc/md5fa: misc/md5fa.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS) - - misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS) - - misc/wgsim: misc/wgsim.o -- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - --misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h) --misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h) --misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h) --misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h) -+misc/ace2sam.o: misc/ace2sam.c config.h -+misc/md5fa.o: misc/md5fa.c config.h -+misc/md5sum-lite.o: misc/md5sum-lite.c config.h -+misc/wgsim.o: misc/wgsim.c config.h - - misc/maq2sam-short.o: misc/maq2sam.c config.h - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild index 5cfcfd7f6a79..d598a3292728 100644 --- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild +++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild @@ -1,11 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit python-single-r1 toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" HOMEPAGE="http://samtools.sourceforge.net/" @@ -14,23 +12,17 @@ SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.g LICENSE="MIT" SLOT="0.1-legacy" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="${PYTHON_DEPS} +RDEPEND=" sys-libs/ncurses:0= dev-lang/perl" -DEPEND="${RDEPEND} - virtual/pkgconfig" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" -PATCHES=( - "${FILESDIR}/${P}-buildsystem.patch" -) +PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) src_prepare() { default - # required, otherwise python_fix_shebang errors out - sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die tc-export CC AR } @@ -44,16 +36,16 @@ src_install() { # install executables and hide them away from sight dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \ misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck} - mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die - mkdir "${ED%/}"/usr/bin || die - mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die + mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die + mkdir "${ED}"/usr/bin || die + mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die - # ... do the same with the python script, but also fix the shebang - mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die - python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py + # remove py2 script, has been removed upstream anyways + # https://github.com/samtools/samtools/issues/1125 + rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die # fix perl shebangs - pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die + pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die local i for i in plot-bamcheck *.pl; do sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die @@ -70,14 +62,12 @@ src_install() { doman ${PN}-${SLOT}.1 einstalldocs - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples } pkg_postinst() { elog "This version of samtools should *not* be your first choice for working" elog "with NGS data. It is installed solely for programs requiring it." - elog "It is recommended that you use >=sci-biology/samtools-1.2." + elog "It is recommended that you use >=sci-biology/samtools-1.10." } diff --git a/sci-biology/samtools/samtools-1.9-r1.ebuild b/sci-biology/samtools/samtools-1.10.ebuild index 0d0f993895fc..0ef5e6c19e8e 100644 --- a/sci-biology/samtools/samtools-1.9-r1.ebuild +++ b/sci-biology/samtools/samtools-1.10.ebuild @@ -12,12 +12,11 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" RDEPEND=" dev-lang/perl =sci-libs/htslib-${PV}* - sys-libs/ncurses:0= + sys-libs/ncurses:0=[unicode] sys-libs/zlib:=" DEPEND="${RDEPEND}" BDEPEND="virtual/pkgconfig" @@ -31,19 +30,27 @@ src_prepare() { eautoreconf } +src_configure() { + econf \ + --with-ncurses \ + --with-htslib=system \ + CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)" +} + +src_compile() { + emake AR="$(tc-getAR)" +} + src_test() { - local -x LD_LIBRARY_PATH="${S}" + # the tview test diffs expect 80-columns output + unset COLUMNS + default } src_install() { default - # varfilter.py has been retired upstream for being py2 only - rm "${ED}"/usr/bin/varfilter.py || die - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples } diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild deleted file mode 100644 index c2bc7ce89cf6..000000000000 --- a/sci-biology/samtools/samtools-1.5.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools python-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}* - sys-libs/ncurses:0= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" ) - -src_prepare() { - default - - python_setup - python_fix_shebang misc/varfilter.py - - # remove bundled htslib - rm -r htslib-* || die - - eautoreconf -} - -src_test() { - local -x LD_LIBRARY_PATH="${S}" - default -} - -src_install() { - default - - # install libbam and headers - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} |