From 2fd57282f0262ca084e05b0f2c63fbada395d02b Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 16 Jan 2022 20:27:28 +0000 Subject: gentoo resync : 16.01.2021 --- sci-biology/Manifest.gz | Bin 21129 -> 20808 bytes sci-biology/abyss/Manifest | 5 +- sci-biology/abyss/abyss-2.0.3-r2.ebuild | 64 ---------- sci-biology/abyss/abyss-2.3.4.ebuild | 57 +++++++++ sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 -- sci-biology/gibbs/Manifest | 4 - sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch | 11 -- sci-biology/gibbs/gibbs-3.1.ebuild | 47 -------- sci-biology/gibbs/metadata.xml | 13 -- sci-biology/picard/Manifest | 4 - sci-biology/picard/files/1.103-gentoo.patch | 131 --------------------- sci-biology/picard/metadata.xml | 11 -- sci-biology/picard/picard-1.103.ebuild | 69 ----------- 13 files changed, 59 insertions(+), 368 deletions(-) delete mode 100644 sci-biology/abyss/abyss-2.0.3-r2.ebuild create mode 100644 sci-biology/abyss/abyss-2.3.4.ebuild delete mode 100644 sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch delete mode 100644 sci-biology/gibbs/Manifest delete mode 100644 sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch delete mode 100644 sci-biology/gibbs/gibbs-3.1.ebuild delete mode 100644 sci-biology/gibbs/metadata.xml delete mode 100644 sci-biology/picard/Manifest delete mode 100644 sci-biology/picard/files/1.103-gentoo.patch delete mode 100644 sci-biology/picard/metadata.xml delete mode 100644 sci-biology/picard/picard-1.103.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 7adf00a4e082..cb256061da9a 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index 72c889e36a57..fe1e04ce4b56 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,4 +1,3 @@ -AUX abyss-2.0.3-prog-AR.patch 350 BLAKE2B 20e1a428ea02c3c67c5df9b92f623ddea58f2054912d0ca788f0a9890057277cd98babe48d089852541db262ab0a69e95ead2a4b31456a62597ae1d4856e8c5e SHA512 747e9d258767c698a95615ae83db18662ec1851c0a6dfcdcec6aea68dc76415e89b3f85f1f8ff6c04fff22052c787a43948f8f3588220e2dc66cc7262788c52a -DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 -EBUILD abyss-2.0.3-r2.ebuild 1556 BLAKE2B a25f93323564ce83b2a15ed31881a873ddafe688f9277439aef25dbb3a76c6d796984105498c2f547bf00229ce4c465d9e5c22c949c543b29fd61c22a8d52568 SHA512 9c5649115d97c8b6aee3909d092f8429c59c31b9200b71023bb05e3bc2501c3f55a1d4b07c9bacbfd94fc6a10a4a5124a6135b743e29d126856796bab5ea1f3f +DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4 +EBUILD abyss-2.3.4.ebuild 1269 BLAKE2B bf4a1edb477650f3d6650c7ae1cfb0d37132215bf8bb4c395a702c506a0d648386168731ad329875380fd46f1a3ccbe673d3211d1ee854538bbe28dbeb49ecb5 SHA512 26a5fec0fbed0c0fdb0f328b993553ec1ceb7632d2d9ad18736f3099df542a88da0d1996c444d3fdbfe59d1dda55161e7de8ea121a22a1bb80c507656999d39c MISC metadata.xml 457 BLAKE2B 7941e6d318c33992a00ce167bf738bea01a1c54b3e8381947757880e34f5a38da9bbd91837a34338f81e6d23e363dbbde734cb5075f6bfcf49a694f19d5a24a8 SHA512 e722cef310475d7e4aae8b0a9e23c73c0ab44acf62e6afdb4355da201565aedbedd2f2100676c6c58218909d60b45b1938c3afe13fff62c4fdfbea0ff2ef6e49 diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild deleted file mode 100644 index b9aed09d3eec..000000000000 --- a/sci-biology/abyss/abyss-2.0.3-r2.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - dev-libs/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch) - -# GHC uses it's own native code generator. Portage's -# QA check generates false positive because it assumes -# presence of GCC-specific sections. -# -# Workaround false positiove by disabling the check completely. -# bug #677600 -QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak' - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -src_prepare() { - default - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) -} diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild new file mode 100644 index 000000000000..c2e1ffd29b32 --- /dev/null +++ b/sci-biology/abyss/abyss-2.3.4.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/" +SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + dev-libs/libffi:0= + ) + sys-cluster/openmpi + dev-db/sqlite:3 +" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + ) +" + +# todo: --enable-maxk=N configure option +# todo: also allow build with mpich (--enable-mpich) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + default + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + # disable building haskell tool Misc/samtobreak + # unless request by user: bug #534412 + use misc-haskell || export ac_cv_prog_ac_ct_GHC= + + econf $(use_enable openmp) --enable-maxk=256 +} diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch deleted file mode 100644 index d41c58ad261a..000000000000 --- a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch +++ /dev/null @@ -1,11 +0,0 @@ -https://bugs.gentoo.org/725300 ---- a/configure.ac -+++ b/configure.ac -@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version]) - AC_CHECK_PROG(PANDOC, pandoc, yes) - AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"]) -+AM_PROG_AR - - # Checks for header files. - AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest deleted file mode 100644 index 2475c8e59888..000000000000 --- a/sci-biology/gibbs/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX gibbs-3.1-fix-CFLAGS.patch 213 BLAKE2B 9a0f7f0412569cef1cce984f5087f7b99e16163ac6c6c3e0aad27f14cd2f7ed5bfb22f21f433f1c343a9e73899dedb00ea93467adc4cc42a3dceae41aa1e3f86 SHA512 afd0fffb891eefe8799025a032a802f398ac737900e1fac86f79964bfe493ee906c3e5f42abc5e45d3de5af80887ab25ef207a885a6ddb8b6fe0d0ab1f906046 -DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52 -EBUILD gibbs-3.1.ebuild 912 BLAKE2B 29d51a769e6a477bb81da6d467a1b2befbfd2f83282184a1087de0a4a5d736a5df01f3767663141bd6282826bd4fcad5ca0ddaea916fc93e582ccd8b4a8e98b8 SHA512 975c0bd3c57a8db25324636ce8f2fd9ef9bde1de4a980ba93fbe3e7bf8362a51f06ae5b1687570d81012ef6eed6536bfde418327a045bcf54a1e1517d85d989f -MISC metadata.xml 484 BLAKE2B d9cd3734d282126d0c50a2b4ac64e5f7dc584150e47a02fad550b3b4e3102018d95c0d226967dae006523ed37da4f3b33a89e6911d237aed54af8a923c7d5f45 SHA512 9a540d968cae036719647f394219ec70184bf956d1c6e6b86e32218426800bad998619e11094ca0d80714b6bbf5b9f37c3edc1397755e0c34bc8b63a16a43655 diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch deleted file mode 100644 index 6eaad637cfc8..000000000000 --- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/configure.in -+++ b/configure.in -@@ -51,7 +51,7 @@ - fi - ]) - --CFLAGS="$OPTFLAGS $MPIFLAGS -Wall -Werror $MACFLAG" -+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG" - - AC_PROG_CC([$COMP_LIST]) - diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild deleted file mode 100644 index a06d0880ee4d..000000000000 --- a/sci-biology/gibbs/gibbs-3.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" -HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html" -SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="mpi" - -DEPEND=" - mpi? ( - virtual/mpi - sys-cluster/mpe2 - )" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch ) - -src_prepare() { - default - mv configure.{in,ac} || die - eautoreconf -} - -src_configure() { - use mpi && export CC=mpicc - econf $(use_enable mpi) -} - -src_install() { - default - - exeinto /usr/$(get_libdir)/${PN} - doexe *.pl -} - -pkg_postinst() { - einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}." - einfo "These scripts require installation of sci-biology/bioperl." -} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml deleted file mode 100644 index a0cd7b42b3ab..000000000000 --- a/sci-biology/gibbs/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - The Gibbs motif sampler stochastically examines candidate alignments - in an effort to find the best alignment as measured by the maximum - a posteriori (MAP) log-likelihood ratio. - - diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest deleted file mode 100644 index 82fc7ef9c66e..000000000000 --- a/sci-biology/picard/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX 1.103-gentoo.patch 5667 BLAKE2B 7d096dfb289a121a9e4cd27614dbf106fcbd17ea39666dd11508c7e58ec098c653c6bfb60ce69f173e3da25963c5d7335affb659566cf43d26f287d2898c37b2 SHA512 966b0cc9ffc5bbf4b23c003538e01533344df496c38797ab84fcd2b382e91e003cc797a0c6ff5a878406b1fc169c1b044bce447b68770c665cec327762f08f6d -DIST picard-1.103.tar.bz2 15037887 BLAKE2B a4df3aad9242749964a997698d80634e14ce19af575de9609655483eba247d0968cbdc856dbf00d854ec7eae37da8f3d047c50e4b78843e9d08441d9ef18eff6 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca -EBUILD picard-1.103.ebuild 1513 BLAKE2B 1755995201677c74108fbc0af289b46c1c518a620b87019adab0f90dd2fa6abc5a4d0135f2883f9716aadb96f60b76199fba109292ae4ff65b29dac82023e119 SHA512 e731bbabeed2d16707ad900a8a271143542c3c851c4becd240d79158b2f806bf5a4faf22b7c466427c406392faefc51628be621ec5b2d429a47a716d003a66c1 -MISC metadata.xml 338 BLAKE2B f32ddb3924bbd34ae207756d7e9b17715cd1b0a87c079201d628cb851c3f1bea487d6953548e1b820148900d0ae2d056ce55408d5d84a4a8f798440b8e4e8a53 SHA512 17119585510e7c19ded9131b140b21c9ae9773e6800d1c2ab56401d15ca995fec7ea3db71d231fc1c90e9f1a22bdc3ed01506fff1411221675c669febde9736b diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch deleted file mode 100644 index 00e89b95056a..000000000000 --- a/sci-biology/picard/files/1.103-gentoo.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/build.xml b/build.xml -index fca2271..11f4fbd 100755 ---- a/build.xml -+++ b/build.xml -@@ -52,9 +52,6 @@ - - - -- -- -- - - - -@@ -78,9 +75,6 @@ - - - -- -- -- - - - -@@ -94,10 +88,6 @@ - - - -- -- -- - - - -@@ -138,7 +128,7 @@ - - - -- -+ - - - - -+ -+ - - - -@@ -165,7 +157,7 @@ - - - - - -@@ -200,13 +192,12 @@ - - - -- - - - - -- - - - -@@ -214,7 +205,7 @@ - - - -- - - -@@ -225,7 +216,7 @@ - - - -- - - -@@ -262,7 +253,7 @@ - - - -- -+ - - - -@@ -344,7 +335,7 @@ - - - -- -+ - - - -@@ -468,8 +459,6 @@ - target="${javac.target}"> - - -- -- - - - -@@ -494,8 +483,6 @@ - - - -- -- - - - diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml deleted file mode 100644 index 22fd62cbaa79..000000000000 --- a/sci-biology/picard/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - picard - - diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild deleted file mode 100644 index 7a6111c87746..000000000000 --- a/sci-biology/picard/picard-1.103.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -JAVA_PKG_IUSE="doc source test" -WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java-based command-line utilities that manipulate SAM files" -HOMEPAGE="http://picard.sourceforge.net/" -SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2" - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -CDEPEND="dev-java/snappy:1.0 - dev-java/cofoja:0 - dev-java/commons-jexl:2 - dev-java/ant-core:0" - -DEPEND=">=virtual/jdk-1.6 - dev-java/ant-apache-bcel:0 - test? ( - dev-java/testng:0 - dev-lang/R - ) - ${CDEPEND}" -RDEPEND=">=virtual/jre-1.6 - ${CDEPEND}" - -EANT_BUILD_TARGET="all" -EANT_TEST_TARGET="test" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" -EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" - -java_prepare() { - mkdir "${S}"/lib || die - - epatch "${FILESDIR}"/${PV}-gentoo.patch - - mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die -} - -src_install() { - cd dist || die - - for i in *-${PV}.jar; do - java-pkg_newjar $i ${i/-${PV}/} - rm $i || die - done - - java-pkg_dojar *.jar - for i in *.jar; do - java-pkg_dolauncher ${i/.jar/} --jar $i; - done - - use source && java-pkg_dosrc "${S}"/src/java/* - use doc && java-pkg_dojavadoc "${S}"/javadoc -} - -src_test() { - java-pkg-2_src_test -} -- cgit v1.2.3