[gentoo-commits] repo/gentoo:master commit in: sci-biology/velvet/

["Justin Lecher" <jlec@gentoo.org>]

commit:     6b672731c97e773142cbc7ee9a5a09cf2c4c5d60
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 14 07:42:19 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Apr 22 16:09:51 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6b672731

sci-biology/velvet: expose additional variables as described in manual and needed at compile time

Package-Manager: Portage-2.3.5, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4421

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/velvet/velvet-1.2.10.ebuild | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
index c6c841be3e4..53f5dd644f9 100644
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -28,9 +28,11 @@ src_prepare() {
 	fi
 	elog "Upstream recommendes using -O3 in CFLAGS"
 	echo
-	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
-	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
-	elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+	elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
+	elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
+	elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
+	elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
+	elog "the package. For example:"
 	elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
 	MAKEOPTS+=" -j1"
 
@@ -51,8 +53,11 @@ src_prepare() {
 		CFLAGS="${CFLAGS}"
 		OPT="${CFLAGS}"
 	)
+	if use openmp; then MAKE_XOPTS+=( OPENMP=1 ); fi
 	if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
 	if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
+	if [[ ${VELVET_BIGASSEMBLY} != "" ]]; then MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} ); fi
+	if [[ ${VELVET_LONGSEQUENCES} != "" ]]; then MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} ); fi
 }
 
 src_compile() {