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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 /sci-biology/bwa/bwa-0.7.16.ebuild
parentsci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added (diff)
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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
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diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild
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+# 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
+}