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authorV3n3RiX <venerix@koprulu.sector>2023-02-24 09:47:15 +0000
committerV3n3RiX <venerix@koprulu.sector>2023-02-24 09:47:15 +0000
commit4003c614d3c4b320c45ab1f4b817459d4709443b (patch)
treefcc0c42e92c56abe0ea39b717b2c3b019c335e41 /sci-biology/bowtie
parent58177544118b9a8393d7501ee5e0e35cd32f2ad4 (diff)
gentoo auto-resync : 24:02:2023 - 09:47:15
Diffstat (limited to 'sci-biology/bowtie')
-rw-r--r--sci-biology/bowtie/Manifest2
-rw-r--r--sci-biology/bowtie/bowtie-2.5.1.ebuild73
2 files changed, 75 insertions, 0 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 9160409c20e7..182f6a8c17fd 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,5 @@
DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
+DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
EBUILD bowtie-2.4.4.ebuild 1207 BLAKE2B 4e89cd7884065637cba84784321100b90a0c0e561dca1519f843be418b33737f31d7db9cc74810a67b1211b9e69e0ac5e7b45548b5b8b0999d42a36a317e9491 SHA512 28473ddcd136172f0b35625cc2a79c4a9a5801c65df28aa0800ed6ea9552f2cf381377ef81504279764fecc7fc2e3c0566c1f7dbc98e2e578ef0452bc2c33653
+EBUILD bowtie-2.5.1.ebuild 1528 BLAKE2B eec523c39c69b9b0862696b0579441c79c028eb2465fdb3c5c153cd1dcaf403e43eb6596bbb64e41f2e7b1fbf27fa832d019720f6c31361d047d4d341e987a6a SHA512 1f7b179a376d0f6a89c223cdf8bc5804b13bef4b9cba3cf4364c109f4d622beba51c2b79f238f92ffb44922711530fbf199af1db36e93d7236b6ce23312e124c
MISC metadata.xml 342 BLAKE2B 7f98f1707e3f53e7c2e532427d6935c692cdcf45304701d28d245ba13b62e752d14d5c3a96925fdf5bceb87a9c291edad0ce715339a5bf92ca6de7ee839adced SHA512 b7f0359b22f70ab25737565bda08e500f6a79bf33052d39fe2013b085c3f636122d0f373430ce3f0b56f95051db9571cb6c79b6f58e30658f45ef752ec708df6
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
new file mode 100644
index 000000000000..353362fd6026
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit python-single-r1 toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+S="${WORKDIR}/${PN}2-${PV}"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="test cpu_flags_x86_sse2 examples"
+# Test script missing from tarball
+# ./scripts/sim/run.sh: No such file or directory
+RESTRICT="test"
+REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ dev-lang/perl
+ sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ app-arch/unzip
+ test? (
+ dev-perl/App-cpanminus
+ dev-perl/B-COW
+ dev-perl/Clone
+ dev-perl/Config-General
+ dev-perl/File-Which
+ dev-perl/local-lib
+ dev-perl/Math-Random
+ dev-perl/Test-Deep
+ dev-perl/Text-Template
+ )
+"
+
+src_compile() {
+ emake \
+ CXX="$(tc-getCXX)" \
+ CXXFLAGS="" \
+ CPPFLAGS="${CPPFLAGS}" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+ dobin bowtie2 bowtie2-*
+
+ exeinto /usr/libexec/bowtie2
+ doexe scripts/*
+
+ HTML_DOCS=( doc/{manual.html,style.css} )
+ einstalldocs
+ dodoc TUTORIAL
+ newman MANUAL bowtie2.1
+
+ python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
+
+ if use examples; then
+ docinto examples
+ dodoc -r example/.
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}