commit: 71c08006931ce9a56edaa201c603d40933498021 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Feb 28 20:04:03 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Feb 28 20:04:03 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=71c08006
sci-biology/bwa: version bump; added a note about a brach of bwa-0.7.13 which has alternative Apache2 license Package-Manager: portage-2.2.26 sci-biology/bwa/bwa-0.7.13.ebuild | 36 +++++++++++++++++++++++++ sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 +++++++++++++++++++ sci-biology/bwa/metadata.xml | 11 ++++++++ 3 files changed, 74 insertions(+) diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.13.ebuild new file mode 100644 index 0000000..27f314b --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.13.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" +HOMEPAGE="http://bio-bwa.sourceforge.net/"; +SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" + +LICENSE="GPL-3" +# bwa-0.7.13 has "Apache2" branch with Apache2-licensed BWA with ropebwt2 index +# feature which is slower than "bwtsw" algorithm but it has a permissive license. +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +PATCHES=( "${FILESDIR}"/${P}-Makefile.patch ) + +src_prepare() { + epatch ${PATCHES[@]} + tc-export CC AR +} + +src_install() { + dobin bwa + + doman bwa.1 + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + dodoc NEWS.md README-alt.md README.md +} diff --git a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch new file mode 100644 index 0000000..406e9b0 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch @@ -0,0 +1,27 @@ +--- Makefile ++++ Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o + AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -26,10 +26,10 @@ + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml new file mode 100644 index 0000000..ceb43ea --- /dev/null +++ b/sci-biology/bwa/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata>
