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

[Martin Mokrejs]

commit:     50c01592d588fb2dadc5e4ca17aefc2943cb9f96
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 18:06:03 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 18:06:03 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=50c01592

sci-biology/Atlas: fix Makefiles at least, will need to unbundle some gzstream library too

Package-Manager: portage-2.2.28

 sci-biology/Atlas/Atlas-2005.ebuild | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index c95df06..4806d1c 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=5
 
+inherit toolchain-funcs
+
 DESCRIPTION="Atlas Whole Genome Assembly Suite"
 HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
 SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
@@ -17,12 +19,16 @@ IUSE=""
 DEPEND="dev-libs/boost"
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}"/atlas-src
+S="${WORKDIR}"/atlas-src/CBT
+
+src_prepare(){
+	sed -e "s/^CC =/CC = $(tc-getCC)/" -e "s/^GCC =/GCC = $(tc-getCXX)/" -i Makefile || die
+	sed -e "s/^GCC =/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
+}
 
 src_compile(){
 	# install headers, bins and libs into CBT_DEVEL_USER, then compile apps
-	cd src || die
-	emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+	emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
 	cd ../CBTApps || die
-	emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+	emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
 }