commit: 32cd1f6f1c693d74575f0c0b5be30bf4d61c1999 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Apr 12 11:22:01 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 12 11:22:01 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=32cd1f6f
sci-biology/picard: version bump (not working yet) Bug: https://github.com/broadinstitute/picard/issues/605 Bug: https://bugs.gentoo.org/653012 Package-Manager: Portage-2.3.27, Repoman-2.3.9 sci-biology/picard/picard-2.10.2.ebuild | 58 ------------------------------ sci-biology/picard/picard-2.17.11.ebuild | 61 ++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+), 58 deletions(-) diff --git a/sci-biology/picard/picard-2.10.2.ebuild b/sci-biology/picard/picard-2.10.2.ebuild deleted file mode 100644 index bddadedbb..000000000 --- a/sci-biology/picard/picard-2.10.2.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -JAVA_PKG_IUSE="doc source" - -inherit 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" - -LICENSE="MIT" -SLOT="0" -IUSE="" -KEYWORDS="" - -CDEPEND="dev-java/snappy:1.1 - dev-java/cofoja:0 - dev-java/commons-jexl:2 - dev-java/ant-core:0 - dev-java/htsjdk:0" - -DEPEND=">=virtual/jdk-1.8 - ${CDEPEND}" - -RDEPEND=">=virtual/jre-1.8 - ${CDEPEND}" - -EANT_BUILD_TARGET="all" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk" - -java_prepare() { - default - rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die - epatch "${FILESDIR}"/${PV}-build.xml.patch -} - -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 --stacktrace --debug || 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 "${S}"/javadoc -#} diff --git a/sci-biology/picard/picard-2.17.11.ebuild b/sci-biology/picard/picard-2.17.11.ebuild new file mode 100644 index 000000000..636bf879c --- /dev/null +++ b/sci-biology/picard/picard-2.17.11.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +#JAVA_PKG_IUSE="doc source" +JAVA_PKG_IUSE="" + +inherit git-r3 java-pkg-2 + +DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files" +HOMEPAGE="http://picard.sourceforge.net + http://broadinstitute.github.io/picard"; +EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"; +EGIT_BRANCH="${PV}" +# building outside of git is not possible, +# see https://github.com/broadinstitute/picard/issues/605 +#SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="" + +CDEPEND="dev-java/snappy:1.1 + dev-java/cofoja:0 + dev-java/commons-jexl:2 + dev-java/htsjdk:0" + +DEPEND=">=virtual/jdk-1.8 + ${CDEPEND}" + +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,htsjdk" + +src_prepare() { + default +} + +src_compile(){ + # work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/ + # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 + # make jure SDK-1.8 is available, JRE-1.8 is not enough + GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die +} + +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 +}
