[gentoo-commits] proj/sci:master commit in: sci-biology/stacks/

[Martin Mokrejs]

commit:     7ce5ca59fd2297afcb385fc468de7f45b44d4210
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec  1 16:36:41 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec  1 16:36:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ce5ca59

sci-biology/stacks: version bump; drop bundled htslib sources, bug #601366

Package-Manager: portage-2.3.2

 .../stacks/{stacks-1.16.ebuild => stacks-1.44.ebuild}  | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/sci-biology/stacks/stacks-1.16.ebuild 
b/sci-biology/stacks/stacks-1.44.ebuild
similarity index 62%
rename from sci-biology/stacks/stacks-1.16.ebuild
rename to sci-biology/stacks/stacks-1.44.ebuild
index d5efc0c..131f562 100644
--- a/sci-biology/stacks/stacks-1.16.ebuild
+++ b/sci-biology/stacks/stacks-1.44.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,9 +6,9 @@ EAPI=5
 
 AUTOTOOLS_AUTORECONF=yes
 
-inherit flag-o-matic eutils perl-module webapp
+inherit flag-o-matic eutils perl-module webapp autotools
 
-DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population 
genomics (RAD-seq Illumina sequencing)"
+DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population 
genomics (RAD-seq sequencing)"
 HOMEPAGE="http://creskolab.uoregon.edu/stacks";
 SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz";
 
@@ -17,16 +17,23 @@ LICENSE="GPL-3"
 KEYWORDS=""
 IUSE=""
 
-# sys-cluster/openmpi
 DEPEND="
+       >=sci-libs/htslib-1.3.1
        dev-cpp/sparsehash
-       sci-biology/samtools
+       sci-biology/samtools:*
        sci-biology/bamtools"
 RDEPEND="${DEPEND}
        dev-lang/perl
        >=dev-lang/php-5
        dev-perl/DBD-mysql"
 
+src_prepare(){
+       sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
+       mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+       sed -e "s#-I./htslib/htslib#-I${mycppflags}#" -i configure.ac || die
+       eautoreconf
+}
+
 src_configure() {
        econf --enable-bam --enable-sparsehash
        webapp_src_preinst
@@ -34,6 +41,7 @@ src_configure() {
 }
 
 src_compile(){
+       rm -rf htslib # zap bundled htslib-1.3.1
        emake DESTDIR="${D}"
 }