From 71deace00d1a2b091313fe137ab7092418c6f87c Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 10 Feb 2020 21:05:55 +0000 Subject: gentoo resync : 10.02.2020 --- sci-biology/tophat/Manifest | 2 +- sci-biology/tophat/tophat-2.1.1-r4.ebuild | 81 ------------------------------ sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 +++++++++++++++++++++++++++++++ 3 files changed, 84 insertions(+), 82 deletions(-) delete mode 100644 sci-biology/tophat/tophat-2.1.1-r4.ebuild create mode 100644 sci-biology/tophat/tophat-2.1.1-r5.ebuild (limited to 'sci-biology/tophat') diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest index 3ae47ce22cb9..391b7baa196a 100644 --- a/sci-biology/tophat/Manifest +++ b/sci-biology/tophat/Manifest @@ -2,5 +2,5 @@ AUX tophat-2.1.1-fix-c++14.patch 655 BLAKE2B 760f2d371e6467340d31c688187a62b0266 AUX tophat-2.1.1-python2-shebangs.patch 758 BLAKE2B 83bda360dc36d3eaa890adee00bdb58698fb5eaaa29255c85b3b63f61536921386115662051a4938d21079a3eb1a103dce752f0320fe1990535d35ae74480fcc SHA512 887e5a8b02c2e43a7fa35c9f98670dd722527c45454ca24d5e2f9d2f372267905d7e0142317769b14830706cf82868cb83ede970ffe527f736d71df794fd6342 AUX tophat-2.1.1-unbundle-seqan-samtools.patch 5224 BLAKE2B acdf26085b6eab54f478f5e31e2f180a008b9a05b853253f8f161759dc79a0fb5ea0c54bbf3a0f4ebf79da71988c60d17899aaa1ff6e927a308eca01edccbdf1 SHA512 d920cee92a0a694a34d6ac5b949e5b883bf9dcff338f36e227cb014732231b96461c02e75418972c85880169751a96c2367f6a4be6ce8c91f310b4b4f6858248 DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc -EBUILD tophat-2.1.1-r4.ebuild 2182 BLAKE2B 31ab114249ef61d7e8fc6d47538483676bb106c9ebebada91236dbb2cfbd9e17aea36d7f480b552ca8a204cae7d6bd10f201ea1ccef7bd23ada5a1758a78b968 SHA512 b97690d43bc89aaafe2df3091602e3509cc1ef4ed2323a58aeb734329f587872325bf73ad69b899d467591bb7be5f685ebeb87376e5fab4b867831b3858c92f0 +EBUILD tophat-2.1.1-r5.ebuild 2222 BLAKE2B 6495a600bb9986ecb5fb2eb09a7c0a5066cc1e28bea0c40df319294dde84a4d08f4eb9e784492f4f416fde4c981d2b6881182439af1a80320eef0ab567a70d7f SHA512 b07baa1225df5a2dbe8d6b031249ab212f815c8710a6d5e74d4a5a9ea8af149e76c045fc1fc943d09b10f7e0e035c899a7a79d7386c73381a0c13f57d6d58e44 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/tophat/tophat-2.1.1-r4.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild deleted file mode 100644 index 590f6eb2d20f..000000000000 --- a/sci-biology/tophat/tophat-2.1.1-r4.ebuild +++ /dev/null @@ -1,81 +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 flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" -HOMEPAGE="https://ccb.jhu.edu/software/tophat/" -SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-libs/boost:=[threads] - dev-python/intervaltree[${PYTHON_USEDEP}] - dev-python/sortedcontainers[${PYTHON_USEDEP}] - sci-biology/samtools:0.1-legacy - sci-biology/bowtie:2" -DEPEND="${RDEPEND} - virtual/pkgconfig - sci-biology/seqan:1.4 - >=sys-devel/autoconf-archive-2016.09.16" - -PATCHES=( - "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch - "${FILESDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-python2-shebangs.patch -) - -src_prepare() { - default - - # remove bundled libs - rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die - - sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ - -i src/tophat.py src/common.cpp || die - - sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ - -e '/^samtools-0\.1\.18\//d' \ - -e '/^SeqAn-1\.4\.2\//d' \ - -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ - -e 's:\$(top_builddir)\/src\/::' \ - -i src/Makefile.am || die - sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die - - # innocuous non-security flags, prevent log pollution - append-cflags -Wno-unused-but-set-variable -Wno-unused-variable - append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" - - # remove ancient autoconf archive macros, wreaking havoc, - # depend on sys-devel/autoconf-archive instead, bug #594810 - rm {ax_boost_thread,ax_boost_base}.m4 || die - - eautoreconf -} - -src_configure() { - econf $(use_enable debug) -} - -src_install() { - default - - # delete bundled python modules - local i - for i in intervaltree sortedcontainers; do - rm -r "${ED%/}"/usr/bin/${i} || die - done -} - -pkg_postinst() { - optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 -} diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild new file mode 100644 index 000000000000..84f3d82b39d0 --- /dev/null +++ b/sci-biology/tophat/tophat-2.1.1-r5.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 toolchain-funcs + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" +HOMEPAGE="https://ccb.jhu.edu/software/tophat/" +SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:=[threads] + $(python_gen_cond_dep ' + dev-python/intervaltree[${PYTHON_MULTI_USEDEP}] + dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}] + ') + sci-biology/samtools:0.1-legacy + sci-biology/bowtie:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sci-biology/seqan:1.4 + >=sys-devel/autoconf-archive-2016.09.16" + +PATCHES=( + "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch + "${FILESDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-python2-shebangs.patch +) + +src_prepare() { + default + + # remove bundled libs + rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die + + sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ + -i src/tophat.py src/common.cpp || die + + sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ + -e '/^samtools-0\.1\.18\//d' \ + -e '/^SeqAn-1\.4\.2\//d' \ + -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ + -e 's:\$(top_builddir)\/src\/::' \ + -i src/Makefile.am || die + sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die + + # innocuous non-security flags, prevent log pollution + append-cflags -Wno-unused-but-set-variable -Wno-unused-variable + append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" + + # remove ancient autoconf archive macros, wreaking havoc, + # depend on sys-devel/autoconf-archive instead, bug #594810 + rm {ax_boost_thread,ax_boost_base}.m4 || die + + eautoreconf +} + +src_configure() { + econf $(use_enable debug) +} + +src_install() { + default + + # delete bundled python modules + local i + for i in intervaltree sortedcontainers; do + rm -r "${ED%/}"/usr/bin/${i} || die + done +} + +pkg_postinst() { + optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 +} -- cgit v1.2.3