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

[Martin Mokrejs]

commit:     edf1cd8c7acd0369e94308ab5cdbcfea6c81e50b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 23 00:47:46 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 23 00:47:46 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=edf1cd8c

sci-biology/augustus: respect EPREFIX and new DEPENDency

The dependency is brought in through the comparative gene prediction
code.

Package-Manager: Portage-2.3.24, Repoman-2.3.6

 sci-biology/augustus/augustus-3.3.ebuild | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
index b050f1da2..b2b19a04e 100644
--- a/sci-biology/augustus/augustus-3.3.ebuild
+++ b/sci-biology/augustus/augustus-3.3.ebuild
@@ -17,7 +17,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="examples"
 
+# TODO: provide USE for mysql and sqlite, edit src/Makefile to reflect paths
+#       and common.mk 
 RDEPEND="
+	sci-mathematics/lpsolve
 	sci-libs/gsl
 	dev-libs/boost
 	sys-libs/zlib"
@@ -30,10 +33,13 @@ src_prepare() {
 	# epatch "${FILESDIR}"/${P}-sane-build.patch
 	tc-export CC CXX
 	sed -e 's/ -O3//g' -i src/Makefile || die
-	# enable comparative gene prediction (needs c++11 compiler)
+	# enable comparative gene prediction (needs c++11 compiler),
+	#    this needs sci-mathematics/lpsolve
 	sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
-	# respect $EPREFIX
-	sed -e 's#^INCLUDES = /usr/include/bamtools#INCLUDES = ${EPREFIX}/usr/include/bamtools#' -i auxprogs/bam2hints/Makefile || die
+	# respect $EPREFIX at src/Makefile, auxprogs/bam2hints/Makefile, more?
+	find . -name Makefile | while read f; do \
+		sed -s 's#/usr/include#${EPREFIX}/usr/include#' -i $f || die;
+	done
 }
 
 src_compile() {