commit: b4649db619f8514efb9377422de3ea42154b3a80 Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Thu Feb 5 19:20:03 2015 +0000 Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> CommitDate: Thu Feb 5 19:20:03 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4649db6
Updated bwa to 0.7.12 and modernized the build system. Removed hard-coded ar. --- sci-biology/bwa/bwa-0.7.12.ebuild | 31 +++++++++++++++++++++++++++++++ sci-biology/bwa/files/bwa_Makefile.patch | 27 +++++++++++++++++++++++++++ sci-biology/bwa/metadata.xml | 5 +++++ 3 files changed, 63 insertions(+) diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild new file mode 100644 index 0000000..353c4bf --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.12.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit base 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/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +PATCHES=( "${FILESDIR}"/${PN}_Makefile.patch ) + +src_compile() { + tc-export CC AR + default +} + +src_install() { + dobin bwa || die + doman bwa.1 || die + exeinto /usr/share/${PN} + doexe qualfa2fq.pl xa2multi.pl || die + dodoc NEWS.md README-alt.md README.md || die +} diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch new file mode 100644 index 0000000..406e9b0 --- /dev/null +++ b/sci-biology/bwa/files/bwa_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..f17a827 --- /dev/null +++ b/sci-biology/bwa/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata>
