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

[Martin Mokrejs]

commit:     59cbe00f7e3f09edbe45448df2f75cbcf2d0e0c0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 30 17:50:55 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 30 17:50:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=59cbe00f

sci-biology/fastqc: version bump, added perl dependency, Apache ant-building does not work still

Package-Manager: portage-2.2.18

 sci-biology/fastqc/ChangeLog                                      | 7 +++++++
 sci-biology/fastqc/{fastqc-0.11.2.ebuild => fastqc-0.11.3.ebuild} | 8 +++++++-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog
index b828a60..3510855 100644
--- a/sci-biology/fastqc/ChangeLog
+++ b/sci-biology/fastqc/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*fastqc-0.11.3 (30 May 2015)
+
+  30 May 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +fastqc-0.11.3.ebuild, -fastqc-0.11.2.ebuild:
+  sci-biology/fastqc: version bump, added perl dependency, Apache ant-building
+  does not work still
+
   05 Mar 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +files/build.xml,
   fastqc-0.11.2.ebuild:
   added build.xml exported by author from Eclipse IDE (it doesn't work under ant

diff --git a/sci-biology/fastqc/fastqc-0.11.2.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
similarity index 82%
rename from sci-biology/fastqc/fastqc-0.11.2.ebuild
rename to sci-biology/fastqc/fastqc-0.11.3.ebuild
index dadc288..d2ae40e 100644
--- a/sci-biology/fastqc/fastqc-0.11.2.ebuild
+++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild
@@ -18,6 +18,7 @@ IUSE=""
 DEPEND="sci-biology/picard
 	>=virtual/jre-1.5:*"
 RDEPEND="${DEPEND}
+	dev-lang/perl
 	>=virtual/jdk-1.5:*
 	dev-java/ant-core"
 
@@ -27,11 +28,16 @@ src_prepare(){
 	cp "${FILESDIR}"/build.xml . || die
 }
 
+src_compile(){
+	ant build || die # TODO: this does not work somehow
+}
+
 src_install(){
 	dobin fastqc run_fastqc.bat
 	dodoc README.txt RELEASE_NOTES.txt
 
 	# TODO: need to compile java in uk/ac/babraham/FastQC/
 	# and decide whether jbzip2-0.9.jar is a standard java lib or not
-	# ignore the sam-1.32.jar, that is likely library already in sci-biology/picard
+	# ignore the sam-1.103.jar, that is likely library already in sci-biology/picard
+	# cisd-jhdf5.jar
 }