commit: c1fb3811426183133b6ee50bc58f03f2a90e93ca Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat May 7 23:17:41 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat May 7 23:17:54 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c1fb3811
sci-biology/bwa: Version bump Package-Manager: portage-2.2.28 sci-biology/bwa/Manifest | 1 + sci-biology/bwa/bwa-0.7.13.ebuild | 38 +++++++++++++++++++++++++ sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 ++++++++++++++++++ 3 files changed, 66 insertions(+) diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index 9c0d995..3cf0fb1 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1 +1,2 @@ DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 +DIST bwa-0.7.13.tar.bz2 189670 SHA256 559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc SHA512 37966e914321d17b5a1d4e3a7786abdd9dd476e4dd7aaf924fb0e0726e3827a1414d9ffccc114a1a334943c8dde38273ce5fafdd1b429ab0f3cbf47ddbd6bedf WHIRLPOOL 86b278b301aa1ff4334c0d78709a61dc034895deb6aa2bd60ee45a595198343e7d60db458c61168b8c61a6ace21db394583b6314a56df3171a151f554c07f769 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..2ce3ff3 --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.13.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit 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/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +RDEPEND="dev-lang/perl" + +PATCHES=( + "${FILESDIR}"/${P}-Makefile.patch +) + +src_prepare() { + default + tc-export CC AR +} + +src_install() { + dobin bwa + + doman bwa.1 + + exeinto /usr/libexec/${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..39b437a --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch @@ -0,0 +1,27 @@ +--- bwa-0.7.13/Makefile ++++ bwa-0.7.13/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)
