* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/
@ 2016-04-24 7:24 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2016-04-24 7:24 UTC (permalink / raw
To: gentoo-commits
commit: bec93ffba2d6dd56c7b10338771a91490bf1ce28
Author: Johann Schmitz <ercpe <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 06:15:26 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 06:15:26 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bec93ffb
sci-biology/picard: brought ebuild for 2.2.2 to a somewhat workable state. Dropped test execution for now.
Package-Manager: portage-2.2.26
sci-biology/picard/files/2.2.2-build.xml.patch | 115 +++++++++++++++++++++++++
sci-biology/picard/picard-2.2.2.ebuild | 48 +++--------
2 files changed, 129 insertions(+), 34 deletions(-)
diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch b/sci-biology/picard/files/2.2.2-build.xml.patch
new file mode 100644
index 0000000..278c4a1
--- /dev/null
+++ b/sci-biology/picard/files/2.2.2-build.xml.patch
@@ -0,0 +1,115 @@
+diff --git a/build.xml b/build.xml
+index f0b98ab..14ff7f7 100755
+--- a/build.xml
++++ b/build.xml
+@@ -83,15 +83,6 @@
+ <!-- INIT -->
+ <target name="init">
+ <path id="classpath">
+- <fileset dir="${htsjdk_lib_dir}">
+- <include name="*.jar"/>
+- <include name="**/*.jar"/>
+- </fileset>
+- <!-- for the specific HTSJDK library JARs -->
+- <fileset dir="${htsjdk}/lib">
+- <include name="*.jar"/>
+- <include name="**/*.jar"/>
+- </fileset>
+ <fileset dir="${lib}">
+ <include name="**/*.jar"/>
+ </fileset>
+@@ -117,53 +108,21 @@
+
+ <!-- HTS-JDK -->
+ <target name="set-htsjdk-version">
+- <!-- set the htsjdk version -->
+- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
+- <loadfile property="htsjdk-version" srcFile="${htsjdk}/htsjdk.version.properties">
+- <filterchain>
+- <linecontains>
+- <contains value="htsjdk-version="/>
+- </linecontains>
+- <tokenfilter>
+- <replacestring from="htsjdk-version=" to=""/>
+- </tokenfilter>
+- <striplinebreaks/>
+- </filterchain>
+- </loadfile>
+ </target>
+
+ <target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge">
+- <exec executable="git" failonerror="true">
+- <arg value="clone"/>
+- <arg value="${htsjdk_git_url}"/>
+- <arg value="${htsjdk}"/>
+- </exec>
+ </target>
+
+ <target name="compile-htsjdk" depends="set-htsjdk-version" description="Build HTS-JDK, and grab build jars">
+- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
+- <ant antfile="build.xml" dir="${htsjdk}" target="all" inheritall="false"/>
+- <copy todir="${htsjdk_lib_dir}">
+- <fileset dir="${htsjdk}/dist" includes="**/*-*.jar"/>
+- <fileset dir="${htsjdk}/lib" includes="*.jar"/>
+- </copy>
+- <copy todir="${dist}">
+- <fileset dir="${htsjdk}/dist" includes="**/*.jar" excludes="**/*-*.jar"/>
+- </copy>
+- <!-- set the htsjdk version -->
+- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
+ </target>
+
+ <target name="clean-htsjdk" description="Clean HTS-JDK">
+- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
+ </target>
+
+ <target name="test-htsjdk" description="Test HTS-JDK">
+- <ant antfile="build.xml" dir="${htsjdk}" target="test" inheritall="false"/>
+ </target>
+
+ <target name="compile-htsjdk-tests" description="Compile HTS-JDK Tests">
+- <ant antfile="build.xml" dir="${htsjdk}" target="compile-tests" inheritall="false"/>
+ </target>
+
+ <!-- COMPILE -->
+@@ -292,15 +251,11 @@
+ <fileset dir="${lib}">
+ <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing -->
+ </fileset>
+- <fileset dir="${htsjdk_lib_dir}">
+- <include name="*.jar"/>
+- </fileset>
+ </unjar>
+
+ <jar destfile="${dist}/picard.jar" compress="no">
+ <fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/>
+ <fileset dir="${src.scripts}" includes="**/*.R"/>
+- <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/>
+ <fileset dir="${dist.tmp}" includes="**/*"/>
+ <fileset dir="${jar_opt}" includes="**/*"/>
+
+@@ -396,13 +351,9 @@
+ <fileset dir="${lib}">
+ <include name="**/*.jar"/>
+ </fileset>
+- <fileset dir="${htsjdk}/dist">
+- <include name="**/*.jar"/>
+- </fileset>
+ </classpath>
+ <fileset dir=".">
+ <include name="${src}/**/*.java"/>
+- <include name="${htsjdk_src}/**/*.java"/>
+ </fileset>
+ <arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/>
+ </javadoc>
+@@ -508,10 +459,8 @@
+ description="Default build target">
+ <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
+ <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
+- <zipfileset dir="${htsjdk_lib_dir}" includes="htsjdk-*.jar" prefix="picard-tools-${picard-version}"/>
+ <zipfileset dir="${lib}" includes="snappy*.jar"/>
+ <!-- distribute libJniDeflater.so in same directory as jarfiles-->
+- <zipfileset dir="${htsjdk}/lib/jni" includes="*" prefix="picard-tools-${picard-version}"/>
+ </zip>
+ </target>
+
diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild
index b9e6917..c43b52c 100644
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ b/sci-biology/picard/picard-2.2.2.ebuild
@@ -2,73 +2,53 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI="5"
+EAPI="6"
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+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://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
IUSE=""
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
-CDEPEND="dev-java/snappy:1.0
+CDEPEND="dev-java/snappy:1.1
dev-java/cofoja:0
dev-java/commons-jexl:2
- dev-java/ant-core:0"
+ dev-java/ant-core:0
+ dev-java/htsjdk:0"
DEPEND=">=virtual/jdk-1.8
- dev-java/ant-apache-bcel:0
- test? (
- dev-java/testng:0
- dev-lang/R
- )
${CDEPEND}"
-# >=jdk8u66
+
RDEPEND=">=virtual/jre-1.8
${CDEPEND}"
EANT_BUILD_TARGET="all"
-EANT_TEST_TARGET="test"
EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
+EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
java_prepare() {
- mkdir -p "${S}"/lib || die
-
- # TODO: update the old patch
- #epatch "${FILESDIR}"/${PV}-gentoo.patch
-
- mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
+ default
+ rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
+ epatch "${FILESDIR}"/${PV}-build.xml.patch
}
src_install() {
cd dist || die
- for i in *-${PV}.jar; do
- java-pkg_newjar $i ${i/-${PV}/}
- rm $i || die
- done
+ java-pkg_dojar ${PN}.jar
+ java-pkg_dojar ${PN}-lib.jar
- java-pkg_dojar *.jar
- for i in *.jar; do
- java-pkg_dolauncher ${i/.jar/} --jar $i;
- done
+ java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
use source && java-pkg_dosrc "${S}"/src/java/*
use doc && java-pkg_dojavadoc "${S}"/javadoc
}
-
-src_test() {
- java-pkg-2_src_test
-}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 2+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
commit: 7395e580724ff8e6c42f83b063e71fea97f4069d
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:08:25 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:08:25 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7395e580
sci-biology/picard: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
sci-biology/picard/files/2.2.2-build.xml.patch | 115 -------------------------
sci-biology/picard/metadata.xml | 16 ----
sci-biology/picard/picard-1.141.ebuild | 72 ----------------
sci-biology/picard/picard-2.18.2.ebuild | 62 -------------
sci-biology/picard/picard-2.2.2.ebuild | 53 ------------
sci-biology/picard/picard-9999.ebuild | 57 ------------
6 files changed, 375 deletions(-)
diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch b/sci-biology/picard/files/2.2.2-build.xml.patch
deleted file mode 100644
index 278c4a1a4..000000000
--- a/sci-biology/picard/files/2.2.2-build.xml.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-diff --git a/build.xml b/build.xml
-index f0b98ab..14ff7f7 100755
---- a/build.xml
-+++ b/build.xml
-@@ -83,15 +83,6 @@
- <!-- INIT -->
- <target name="init">
- <path id="classpath">
-- <fileset dir="${htsjdk_lib_dir}">
-- <include name="*.jar"/>
-- <include name="**/*.jar"/>
-- </fileset>
-- <!-- for the specific HTSJDK library JARs -->
-- <fileset dir="${htsjdk}/lib">
-- <include name="*.jar"/>
-- <include name="**/*.jar"/>
-- </fileset>
- <fileset dir="${lib}">
- <include name="**/*.jar"/>
- </fileset>
-@@ -117,53 +108,21 @@
-
- <!-- HTS-JDK -->
- <target name="set-htsjdk-version">
-- <!-- set the htsjdk version -->
-- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
-- <loadfile property="htsjdk-version" srcFile="${htsjdk}/htsjdk.version.properties">
-- <filterchain>
-- <linecontains>
-- <contains value="htsjdk-version="/>
-- </linecontains>
-- <tokenfilter>
-- <replacestring from="htsjdk-version=" to=""/>
-- </tokenfilter>
-- <striplinebreaks/>
-- </filterchain>
-- </loadfile>
- </target>
-
- <target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge">
-- <exec executable="git" failonerror="true">
-- <arg value="clone"/>
-- <arg value="${htsjdk_git_url}"/>
-- <arg value="${htsjdk}"/>
-- </exec>
- </target>
-
- <target name="compile-htsjdk" depends="set-htsjdk-version" description="Build HTS-JDK, and grab build jars">
-- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
-- <ant antfile="build.xml" dir="${htsjdk}" target="all" inheritall="false"/>
-- <copy todir="${htsjdk_lib_dir}">
-- <fileset dir="${htsjdk}/dist" includes="**/*-*.jar"/>
-- <fileset dir="${htsjdk}/lib" includes="*.jar"/>
-- </copy>
-- <copy todir="${dist}">
-- <fileset dir="${htsjdk}/dist" includes="**/*.jar" excludes="**/*-*.jar"/>
-- </copy>
-- <!-- set the htsjdk version -->
-- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
- </target>
-
- <target name="clean-htsjdk" description="Clean HTS-JDK">
-- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
- </target>
-
- <target name="test-htsjdk" description="Test HTS-JDK">
-- <ant antfile="build.xml" dir="${htsjdk}" target="test" inheritall="false"/>
- </target>
-
- <target name="compile-htsjdk-tests" description="Compile HTS-JDK Tests">
-- <ant antfile="build.xml" dir="${htsjdk}" target="compile-tests" inheritall="false"/>
- </target>
-
- <!-- COMPILE -->
-@@ -292,15 +251,11 @@
- <fileset dir="${lib}">
- <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing -->
- </fileset>
-- <fileset dir="${htsjdk_lib_dir}">
-- <include name="*.jar"/>
-- </fileset>
- </unjar>
-
- <jar destfile="${dist}/picard.jar" compress="no">
- <fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/>
- <fileset dir="${src.scripts}" includes="**/*.R"/>
-- <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/>
- <fileset dir="${dist.tmp}" includes="**/*"/>
- <fileset dir="${jar_opt}" includes="**/*"/>
-
-@@ -396,13 +351,9 @@
- <fileset dir="${lib}">
- <include name="**/*.jar"/>
- </fileset>
-- <fileset dir="${htsjdk}/dist">
-- <include name="**/*.jar"/>
-- </fileset>
- </classpath>
- <fileset dir=".">
- <include name="${src}/**/*.java"/>
-- <include name="${htsjdk_src}/**/*.java"/>
- </fileset>
- <arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/>
- </javadoc>
-@@ -508,10 +459,8 @@
- description="Default build target">
- <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
- <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
-- <zipfileset dir="${htsjdk_lib_dir}" includes="htsjdk-*.jar" prefix="picard-tools-${picard-version}"/>
- <zipfileset dir="${lib}" includes="snappy*.jar"/>
- <!-- distribute libJniDeflater.so in same directory as jarfiles-->
-- <zipfileset dir="${htsjdk}/lib/jni" includes="*" prefix="picard-tools-${picard-version}"/>
- </zip>
- </target>
-
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
deleted file mode 100644
index 1d81f108f..000000000
--- a/sci-biology/picard/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>ercpe@gentoo.org</email>
- <name>Johann Schmitz (ercpe)</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">broadinstitute/picard</remote-id>
- <remote-id type="sourceforge">picard</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild
deleted file mode 100644
index 68b10a73d..000000000
--- a/sci-biology/picard/picard-1.141.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
-
-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://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0" # 2.2.2 is MIT instead, not sure when it changed away from Apache
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/snappy:1.0
- dev-java/cofoja:0
- dev-java/commons-jexl:2
- dev-java/ant-core:0"
-
-DEPEND=">=virtual/jdk-1.7
- dev-java/ant-apache-bcel:0
- test? (
- dev-java/testng:0
- dev-lang/R
- )
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.7
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_TEST_TARGET="test"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
-
-java_prepare() {
- mkdir -p "${S}"/lib || die
-
- # TODO: update the patch
- #epatch "${FILESDIR}"/${PV}-gentoo.patch
-
- mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
-}
-
-src_install() {
- cd dist || die
-
- for i in *-${PV}.jar; do
- java-pkg_newjar $i ${i/-${PV}/}
- rm $i || die
- done
-
- java-pkg_dojar *.jar
- for i in *.jar; do
- java-pkg_dolauncher ${i/.jar/} --jar $i;
- done
-
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
-
-src_test() {
- java-pkg-2_src_test
-}
diff --git a/sci-biology/picard/picard-2.18.2.ebuild b/sci-biology/picard/picard-2.18.2.ebuild
deleted file mode 100644
index 9292b1e19..000000000
--- a/sci-biology/picard/picard-2.18.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-#JAVA_PKG_IUSE="doc source"
-JAVA_PKG_IUSE=""
-
-inherit git-r3 java-pkg-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
- http://broadinstitute.github.io/picard"
-EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
-EGIT_COMMIT="${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 $HOME/.m2/
- # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
- # make jure SDK-1.8 is available, JRE-1.8 is not enough
- # see more gradlew arg options in build.xml, especially jar versus shadowJar
- GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug compileJava jar || 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 "${S}"/javadoc
-}
diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild
deleted file mode 100644
index c2bfb0503..000000000
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
- http://broadinstitute.github.io/picard"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-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_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-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
deleted file mode 100644
index 57bbfdb9f..000000000
--- a/sci-biology/picard/picard-9999.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# 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"
-
-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 || 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
-}
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2020-09-22 11:12 [gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/ Aisha Tammy
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2016-04-24 7:24 Justin Lecher
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