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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     3a1f44b97d5e3f2579efe5b83c93cf3114835c84
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 08:49:25 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 08:49:25 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a1f44b9

sci-biology/genometools: disable building using bundled libs

The build packaging system is suboptimal. Hand-edit the Makefile
to force use of shared libs from system-wide. This brings us
to a non-functional package because two lua-based packages are
not yet in the tree.

https://github.com/genometools/genometools/issues/742
https://github.com/genometools/genometools/pull/748

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/genometools/genometools-1.5.10.ebuild | 26 +++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 23fe474e2..026eabc48 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -9,16 +9,34 @@ SRC_URI="http://genometools.org/pub/${P}.tar.gz"
 
 LICENSE="ICS"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
+IUSE="cairo"
 
 DEPEND="
 	dev-libs/glib
 	x11-libs/pango
-	x11-libs/cairo"
+	cairo? ( x11-libs/cairo )
+	sci-biology/samtools:0.1-legacy
+	dev-db/sqlite:3
+	dev-lang/lua
+	dev-lua/lpeg
+	dev-lua/luafilesystem
+	dev-libs/tre"
+# http://keplerproject.github.io/md5/
+# http://keplerproject.org/cgilua
 RDEPEND="${DEPEND}"
 
 src_prepare(){
-	sed -e "s#/usr/local#"${EPREFIX}"/usr#" -i Makefile || die
+	sed -e "s#/usr/local#"${EPREFIX}"/usr#g" -i Makefile || die
+	sed -e "s#/usr/include/bam#${EPREFIX}/usr/include/bam-0.1-legacy#" -i Makefile || die
+	sed -e "s#-lbam#-lbam-0.1-legacy#" -i Makefile || die
 	eapply_user
 }
+
+src_compile(){
+	local myemakeargs=( useshared=yes )
+	! use cairo && myemakeargs+=( cairo=no )
+	use x86 && myemakeargs+=( 32bit=yes )
+	use amd64 && myemakeargs+=( 64bit=yes )
+	emake ${myemakeargs}
+}