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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/bowtie
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/bowtie')
-rw-r--r--sci-biology/bowtie/Manifest2
-rw-r--r--sci-biology/bowtie/bowtie-0.12.8.ebuild44
-rw-r--r--sci-biology/bowtie/bowtie-1.0.0.ebuild42
-rw-r--r--sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch45
-rw-r--r--sci-biology/bowtie/metadata.xml8
5 files changed, 141 insertions, 0 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
new file mode 100644
index 000000000000..1345a9e07e4e
--- /dev/null
+++ b/sci-biology/bowtie/Manifest
@@ -0,0 +1,2 @@
+DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
+DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000000000000..c26c986ed194
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS=""
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL
+}
diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild
new file mode 100644
index 000000000000..b8181190243c
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.0.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL doc/README
+ dohtml doc/{manual.html,style.css}
+}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
new file mode 100644
index 000000000000..3c8a1e1d9ca4
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
@@ -0,0 +1,45 @@
+ alphabet.h | 24 ++++++++++++------------
+ 1 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/alphabet.h b/alphabet.h
+index b464ddf..08d0281 100644
+--- a/alphabet.h
++++ b/alphabet.h
+@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
+ return s_rc;
+ }
+
++/// Reverse a string in-place
++template <typename TStr>
++static inline void reverseInPlace(TStr& s) {
++ typedef typename Value<TStr>::Type TVal;
++ size_t len = length(s);
++ for(size_t i = 0; i < (len>>1); i++) {
++ TVal tmp = s[i];
++ s[i] = s[len-i-1];
++ s[len-i-1] = tmp;
++ }
++}
++
+ /**
+ * Reverse-complement s in-place. Ns go to Ns.
+ */
+@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ }
+ }
+
+-/// Reverse a string in-place
+-template <typename TStr>
+-static inline void reverseInPlace(TStr& s) {
+- typedef typename Value<TStr>::Type TVal;
+- size_t len = length(s);
+- for(size_t i = 0; i < (len>>1); i++) {
+- TVal tmp = s[i];
+- s[i] = s[len-i-1];
+- s[len-i-1] = tmp;
+- }
+-}
+-
+ /**
+ * Return the reverse-complement of s.
+ */
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
new file mode 100644
index 000000000000..e493417070fb
--- /dev/null
+++ b/sci-biology/bowtie/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">bowtie-bio</remote-id>
+ </upstream>
+</pkgmetadata>