[gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/

[Martin Mokrejs]

commit:     ca813e4a288c12c2fee6734cd97c73e86e129920
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 31 11:25:53 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 31 11:25:53 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca813e4a

sci-biology/bwa: version bump

Release 0.7.16 (30 July 2017)
-----------------------------

This release added a couple of minor features and incorporated multiple pull
requests, including:

 * Added option -5, which is useful to some Hi-C pipelines.

 * Fixed an error with samtools sorting (#129). Updated download link for
   GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple
   issues via a collected pull request #139 by @jmarshall. Avoid malformatted
   SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).

This release is expected to give the same alignment as 0.7.15, except the added
mate-cigar tag.

(0.7.16: 30 July 2017, r1180)

https://lists.sourceforge.net/lists/listinfo/bio-bwa-help

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/bwa/bwa-0.7.16.ebuild               | 36 +++++++++++++++++++++++++
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 +++++++++++++++++++
 sci-biology/bwa/metadata.xml                    | 11 ++++++++
 3 files changed, 74 insertions(+)

diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild
new file mode 100644
index 000000000..1568adff3
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.16.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+RDEPEND="dev-lang/perl"
+
+DOCS=( NEWS.md README-alt.md README.md )
+PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch )
+
+src_configure() {
+	tc-export CC AR
+	default
+}
+
+src_install() {
+	dobin bwa
+
+	doman bwa.1
+
+	exeinto /usr/libexec/${PN}
+	doexe qualfa2fq.pl xa2multi.pl
+
+	einstalldocs
+}

diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
new file mode 100644
index 000000000..39b437a02
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.15-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)

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@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">bio-bwa</remote-id>
+  </upstream>
+</pkgmetadata>