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commit: b4649db619f8514efb9377422de3ea42154b3a80 |
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Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> |
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AuthorDate: Thu Feb 5 19:20:03 2015 +0000 |
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Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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CommitDate: Thu Feb 5 19:20:03 2015 +0000 |
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URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4649db6 |
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|
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Updated bwa to 0.7.12 and modernized the build system. Removed hard-coded ar. |
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|
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--- |
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sci-biology/bwa/bwa-0.7.12.ebuild | 31 +++++++++++++++++++++++++++++++ |
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sci-biology/bwa/files/bwa_Makefile.patch | 27 +++++++++++++++++++++++++++ |
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sci-biology/bwa/metadata.xml | 5 +++++ |
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3 files changed, 63 insertions(+) |
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|
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diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild |
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new file mode 100644 |
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index 0000000..353c4bf |
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--- /dev/null |
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+++ b/sci-biology/bwa/bwa-0.7.12.ebuild |
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@@ -0,0 +1,31 @@ |
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+# Copyright 1999-2015 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: $ |
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+ |
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+EAPI=5 |
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+ |
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+inherit base toolchain-funcs |
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+ |
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+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" |
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+HOMEPAGE="http://bio-bwa.sourceforge.net/" |
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+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+IUSE="" |
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+KEYWORDS="~amd64 ~x86 ~x64-macos" |
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+ |
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+PATCHES=( "${FILESDIR}"/${PN}_Makefile.patch ) |
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+ |
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+src_compile() { |
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+ tc-export CC AR |
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+ default |
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+} |
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+ |
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+src_install() { |
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+ dobin bwa || die |
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+ doman bwa.1 || die |
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+ exeinto /usr/share/${PN} |
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+ doexe qualfa2fq.pl xa2multi.pl || die |
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+ dodoc NEWS.md README-alt.md README.md || die |
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+} |
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|
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diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch |
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new file mode 100644 |
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index 0000000..406e9b0 |
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--- /dev/null |
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+++ b/sci-biology/bwa/files/bwa_Makefile.patch |
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@@ -0,0 +1,27 @@ |
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+--- Makefile |
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++++ Makefile |
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+@@ -1,8 +1,8 @@ |
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+-CC= gcc |
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++CC?= gcc |
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+ #CC= clang --analyze |
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+-CFLAGS= -g -Wall -Wno-unused-function -O2 |
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++CFLAGS?= -g -Wall -Wno-unused-function -O2 |
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+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS |
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+-AR= ar |
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++AR?= ar |
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+ DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) |
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+ LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o |
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+ AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ |
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+@@ -26,10 +26,10 @@ |
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+ all:$(PROG) |
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+ |
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+ bwa:libbwa.a $(AOBJS) main.o |
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+- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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+ |
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+ bwamem-lite:libbwa.a example.o |
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+- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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+ |
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+ libbwa.a:$(LOBJS) |
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+ $(AR) -csru $@ $(LOBJS) |
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|
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diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml |
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new file mode 100644 |
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index 0000000..f17a827 |
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--- /dev/null |
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+++ b/sci-biology/bwa/metadata.xml |
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@@ -0,0 +1,5 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <herd>sci-biology</herd> |
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+</pkgmetadata> |
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