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

[Martin Mokrejs]

commit:     2272938e78efe357468c8e1b4c3420f6bfe73284
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:34:47 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:34:47 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2272938e

sci-biology/stacks:

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/stacks/stacks-1.44.ebuild | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
index a7ac01a1f..a4d473e91 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-1.44.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -29,15 +29,16 @@ RDEPEND="${DEPEND}
 
 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${mycppflags}#" -i configure.ac || die
+	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+	if [ -z "$mycppflags" ]; then mycppflags="."; fi
+	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
 	eautoreconf
 }
 
 src_configure() {
 	econf --enable-bam --enable-sparsehash
 	webapp_src_preinst
-	sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
+	sed -i 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' Makefile || die
 }
 
 src_compile(){