aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-07-31 13:25:53 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-07-31 13:25:53 +0200
commitca813e4a288c12c2fee6734cd97c73e86e129920 (patch)
tree81e1dc7facebef46aff6653d3acd1d3caba695db
parentsci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added (diff)
downloadsci-ca813e4a288c12c2fee6734cd97c73e86e129920.zip
sci-ca813e4a288c12c2fee6734cd97c73e86e129920.tar.gz
sci-ca813e4a288c12c2fee6734cd97c73e86e129920.tar.bz2
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
-rw-r--r--sci-biology/bwa/Manifest1
-rw-r--r--sci-biology/bwa/bwa-0.7.16.ebuild36
-rw-r--r--sci-biology/bwa/files/bwa-0.7.15-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 0000000..b46b6d9
--- /dev/null
+++ b/sci-biology/bwa/Manifest
@@ -0,0 +1 @@
+DIST bwa-0.7.16.tar.bz2 191915 SHA256 4b7da7991b9fc105bea5ef37a1db77cdf91f8039b623182627316f896e008cd4 SHA512 50ae72298dc8e450a4f9d5a337d4f3e510625d02f92b570d908db04161e4cbdd22759220b519cb6b6fd73d205e92346ef2d6ed857a4797a978d3709010637000 WHIRLPOOL 66961ce29afd7d642e32a651373a6425c2917844dfd9a2d9b972546e64c5dfe232193809c03cbd6d3686c8a11c712b4c5054fc669c98fbc0e0a4a7a6069ccaba
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 0000000..1568adf
--- /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 0000000..39b437a
--- /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 0000000..ceb43ea
--- /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>