diff options
| -rw-r--r-- | sci-biology/picard/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/picard/picard-1.141.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/picard/picard-2.2.2.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/picard/picard-2.8.1.ebuild | 59 |
4 files changed, 62 insertions, 2 deletions
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest index 91a5492dd..0b6c7208b 100644 --- a/sci-biology/picard/Manifest +++ b/sci-biology/picard/Manifest @@ -1,2 +1,3 @@ DIST picard-1.141.tar.gz 5692255 SHA256 128e761b4dbedda9a89cceb4d1648be213ec823ff105a35db9c9526955a42320 SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4 WHIRLPOOL 5716cc51da6e94b338aceb5a3d01da5ae048f011e3d3eee72a96144d4b6f80dddf898ea902fae08b127f93c771f521437bd299bdeaf005af6f24c76f9844b63d DIST picard-2.2.2.tar.gz 6565857 SHA256 1d858fde23aa9938a87cd96e6c2fbbfcdea669c9f30d524c107af26bce3798de SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b WHIRLPOOL 69df60c171a5e531b78ad670b260d717a749012d05028e1afba2484eb3a84a71e61ade13c7298b0e9bc6ff526367ca886d9440b996882d3f19455f8f46e3bd4f +DIST picard-2.8.1.tar.gz 3851366 SHA256 780d43230f769e312ccc00b0a5bde4f0d8a2020e98e7447887f581550f4cb975 SHA512 897ec512b3bf66c25dd4f1cbb70306cdfd951c9a257f745ae23f7b8bf7125563460f90128b053977c13fa4fb509b5fa4ec6a11d410487fa0c8927b6ab1bd909a WHIRLPOOL 71b1a7c56f465c7afbdc9b8e0143ab2cb0f661edbaa425d07efe264c37cd58adf1f9f7d388e81fbc3a78efe06af5c1c2611feaeaea7bd64bb748709bf515dc43 diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild index ab65edb40..b84d91dbb 100644 --- a/sci-biology/picard/picard-1.141.ebuild +++ b/sci-biology/picard/picard-1.141.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild index c43b52cac..f0cc489c6 100644 --- a/sci-biology/picard/picard-2.2.2.ebuild +++ b/sci-biology/picard/picard-2.2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.8.1.ebuild new file mode 100644 index 000000000..4d09e8d48 --- /dev/null +++ b/sci-biology/picard/picard-2.8.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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 build || 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 +#} |