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 +}