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commit: 7ce5ca59fd2297afcb385fc468de7f45b44d4210 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Thu Dec 1 16:36:41 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Thu Dec 1 16:36:41 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ce5ca59 |
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|
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sci-biology/stacks: version bump; drop bundled htslib sources, bug #601366 |
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|
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Package-Manager: portage-2.3.2 |
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|
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.../stacks/{stacks-1.16.ebuild => stacks-1.44.ebuild} | 18 +++++++++++++----- |
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1 file changed, 13 insertions(+), 5 deletions(-) |
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|
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diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.44.ebuild |
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similarity index 62% |
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rename from sci-biology/stacks/stacks-1.16.ebuild |
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rename to sci-biology/stacks/stacks-1.44.ebuild |
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index d5efc0c..131f562 100644 |
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--- a/sci-biology/stacks/stacks-1.16.ebuild |
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+++ b/sci-biology/stacks/stacks-1.44.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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+# Copyright 1999-2016 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Id$ |
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|
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@@ -6,9 +6,9 @@ EAPI=5 |
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|
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AUTOTOOLS_AUTORECONF=yes |
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|
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-inherit flag-o-matic eutils perl-module webapp |
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+inherit flag-o-matic eutils perl-module webapp autotools |
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|
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-DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population genomics (RAD-seq Illumina sequencing)" |
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+DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics (RAD-seq sequencing)" |
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HOMEPAGE="http://creskolab.uoregon.edu/stacks" |
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SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz" |
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|
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@@ -17,16 +17,23 @@ LICENSE="GPL-3" |
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KEYWORDS="" |
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IUSE="" |
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|
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-# sys-cluster/openmpi |
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DEPEND=" |
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+ >=sci-libs/htslib-1.3.1 |
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dev-cpp/sparsehash |
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- sci-biology/samtools |
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+ sci-biology/samtools:* |
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sci-biology/bamtools" |
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RDEPEND="${DEPEND} |
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dev-lang/perl |
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>=dev-lang/php-5 |
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dev-perl/DBD-mysql" |
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|
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+src_prepare(){ |
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+ sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die |
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+ mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366 |
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+ sed -e "s#-I./htslib/htslib#-I${mycppflags}#" -i configure.ac || die |
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+ eautoreconf |
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+} |
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+ |
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src_configure() { |
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econf --enable-bam --enable-sparsehash |
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webapp_src_preinst |
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@@ -34,6 +41,7 @@ src_configure() { |
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} |
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|
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src_compile(){ |
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+ rm -rf htslib # zap bundled htslib-1.3.1 |
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emake DESTDIR="${D}" |
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} |