aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2016-02-28 21:04:03 +0100
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2016-02-28 21:04:03 +0100
commit71c08006931ce9a56edaa201c603d40933498021 (patch)
tree710a2f0ea2ff4d1024995d3aa0d17ed9fcb8800b /sci-biology/bwa
parentsci-biology/BRAKER: add einfo referring to GeneMark-ET requirement (diff)
downloadsci-71c08006931ce9a56edaa201c603d40933498021.tar.gz
sci-71c08006931ce9a56edaa201c603d40933498021.tar.bz2
sci-71c08006931ce9a56edaa201c603d40933498021.zip
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
Diffstat (limited to 'sci-biology/bwa')
-rw-r--r--sci-biology/bwa/Manifest1
-rw-r--r--sci-biology/bwa/bwa-0.7.13.ebuild36
-rw-r--r--sci-biology/bwa/files/bwa-0.7.13-Makefile.patch27
-rw-r--r--sci-biology/bwa/metadata.xml11
4 files changed, 75 insertions, 0 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
new file mode 100644
index 000000000..5e46094ed
--- /dev/null
+++ b/sci-biology/bwa/Manifest
@@ -0,0 +1 @@
+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 000000000..27f314b7b
--- /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 000000000..406e9b052
--- /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 000000000..ceb43ead2
--- /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-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">bio-bwa</remote-id>
+ </upstream>
+</pkgmetadata>