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

[Martin Mokrejs]

commit:     cc5f20a95234b3565df52116900041d251625751
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:07:39 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:07:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc5f20a9

 sci-biology/igv-2.3.80: version bump, not working yet (upstream github issue 
#293)

Package-Manager: portage-2.3.0

 sci-biology/igv/{igv-2.3.52.ebuild => igv-2.3.80.ebuild} | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.52.ebuild 
b/sci-biology/igv/igv-2.3.80.ebuild
similarity index 80%
rename from sci-biology/igv/igv-2.3.52.ebuild
rename to sci-biology/igv/igv-2.3.80.ebuild
index 9318aa4..55697a9 100644
--- a/sci-biology/igv/igv-2.3.52.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -27,7 +27,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/";
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64"
+KEYWORDS=""
 
 COMMON_DEPS="
        dev-java/absolutelayout
@@ -52,7 +52,7 @@ DEPEND=">=virtual/jdk-1.7
 RDEPEND=">=virtual/jre-1.7
        ${COMMON_DEPS}"
 
-S="${WORKDIR}/igv-${PV}"
+S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you 
fetched wrong file with the precompiled jar
 
 EANT_BUILD_TARGET="all"
 JAVA_ANT_REWRITE_CLASSPATH="true"
@@ -66,12 +66,10 @@ java_prepare() {
        mv lib oldlib || die
        mkdir lib || die
 
-       mv -v 
oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar}
 lib || die
+       mv -v 
oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar}
 lib || die
        mv -v oldlib/batik* lib || die
 
        rm -rvf oldlib/* || die
-
-       epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
 }
 
 src_install() {
@@ -81,3 +79,7 @@ src_install() {
 
        java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
 }
+
+pkg_postinst(){
+       einfo "You may want to install sci-biology/blat for easy sequence 
searches inside igv"
+}