commit: 7d63183f97ac775659f864b49b981e5b56607065
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 12 00:33:30 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 12 00:33:30 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d63183f
sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from
openmpi package
Package-Manager: portage-2.2.18
sci-biology/BBmap/BBmap-34.56.ebuild | 11 ++++++-----
sci-biology/BBmap/ChangeLog | 4 ++++
2 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild
b/sci-biology/BBmap/BBmap-34.56.ebuild
index f95b7e9..43e6236 100644
--- a/sci-biology/BBmap/BBmap-34.56.ebuild
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -15,7 +15,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-# needs USE=java, see bug #542700
DEPEND="
sys-cluster/openmpi[java]
>=virtual/jdk-1.7:*
@@ -25,10 +24,12 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"/bbmap
-#src_prepare(){
-# # fix the line in build.xml to point to mpi.jar location
-# # <property name="mpijar" location="/tmp/mpi.jar" ></property>
-#}
+src_prepare(){
+ # fix the line in build.xml to point to mpi.jar location
+ # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+ # see bug #542700
+ sed -e
's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#'
-i build.xml
+}
src_compile(){
ant dist || die
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 9dcb3f4..315b333 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 12 Nov 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> BBmap-34.56.ebuild:
+ sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from
+ openmpi package
+
09 Mar 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> BBmap-34.56.ebuild:
new package, needs openmpi with java support to provide mpi.jar, see bug
#542700
