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| author |   Ted Tanberry <ted.tanberry@gmail.com> | 2015-02-05 20:20:03 +0100 |
|---|---|---|
| committer | Ted Tanberry <ted.tanberry@gmail.com> | 2015-02-05 20:20:03 +0100 |
| commit | b4649db619f8514efb9377422de3ea42154b3a80 (patch) | |
| tree | 21fcb4fc0fb477238c4ce29f6336c1fd8605f595 | |
| parent | Fixed emboss-r1.eclass to depend on virtual/mysql and not dev-db/mysql. (diff) | |
| download | sci-b4649db619f8514efb9377422de3ea42154b3a80.tar.gz sci-b4649db619f8514efb9377422de3ea42154b3a80.tar.bz2 sci-b4649db619f8514efb9377422de3ea42154b3a80.zip | |
Updated bwa to 0.7.12 and modernized the build system. Removed hard-coded ar.
| -rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.12.ebuild | 31 | ||||
| -rw-r--r-- | sci-biology/bwa/files/bwa_Makefile.patch | 27 | ||||
| -rw-r--r-- | sci-biology/bwa/metadata.xml | 5 |
4 files changed, 64 insertions, 0 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000..9c0d995bf --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1 @@ +DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 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 000000000..353c4bf93 --- /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 000000000..406e9b052 --- /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 000000000..f17a827e3 --- /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> |