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

[Martin Mokrejs]

commit:     716ca9a7f85713e713e0f975ed61cbce194a0a67
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 11 23:22:39 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 11 23:22:39 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=716ca9a7

sci-biology/picard-2.8.1: version bump, do not compile tests by default

Also add a live ebuild so we can test upstream with the gradle build
system.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/picard/picard-2.8.1.ebuild             |  2 +-
 .../{picard-2.8.1.ebuild => picard-9999.ebuild}    | 29 +++++++++++-----------
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/sci-biology/picard/picard-2.8.1.ebuild 
b/sci-biology/picard/picard-2.8.1.ebuild
index 4d09e8d..7f8b3fd 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-2.8.1.ebuild
@@ -44,7 +44,7 @@ java_prepare() {
 src_compile(){
        # work around gradle writing $HOME/.gradle and requiring $HOME/.git
        # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-       GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+       GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 
 #src_install() {

diff --git a/sci-biology/picard/picard-2.8.1.ebuild 
b/sci-biology/picard/picard-9999.ebuild
similarity index 68%
copy from sci-biology/picard/picard-2.8.1.ebuild
copy to sci-biology/picard/picard-9999.ebuild
index 4d09e8d..3df5d98 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-9999.ebuild
@@ -4,14 +4,15 @@
 
 EAPI="6"
 
-JAVA_PKG_IUSE="doc source"
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
 
-inherit java-pkg-2 java-ant-2
+inherit git-r3 java-pkg-2 java-ant-2
 
 DESCRIPTION="Java-based command-line utilities that manipulate 
SAM/BAM/CRAM/VCF files"
 HOMEPAGE="http://picard.sourceforge.net
        http://broadinstitute.github.io/picard";
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> 
${P}.tar.gz"
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git";
 
 LICENSE="MIT"
 SLOT="0"
@@ -44,16 +45,16 @@ java_prepare() {
 src_compile(){
        # work around gradle writing $HOME/.gradle and requiring $HOME/.git
        # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-       GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+       GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 
-#src_install() {
-#      cd dist || die
-#      java-pkg_dojar ${PN}.jar
-#      java-pkg_dojar ${PN}-lib.jar
-#      
-#      java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-#      
-#      use source && java-pkg_dosrc "${S}"/src/java/*
-#      use doc && java-pkg_dojavadoc "${S}"/javadoc
-#}
+src_install() {
+       cd build/libs || die
+       java-pkg_dojar "${PN}".jar
+       java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
+
+       java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+
+       #use source && java-pkg_dosrc "${S}"/src/java/*
+       #use doc && java-pkg_dojavadoc "${S}"/javadoc
+}