sci-biology/picard: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>

7 files changed, 0 insertions, 377 deletions

diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
deleted file mode 100644
index 2f14e87a2..000000000
--- a/sci-biology/picard/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST picard-1.141.tar.gz 5692255 BLAKE2B 26bb6edd32b75895a52c549e61e5873b6b5d1127fa1458e671b24a2b792c86bb3db5f9f8b8f24f9419a4ce1680f6bbad98da8dc7da4bf9b14178e901a28d803e SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4
-DIST picard-2.2.2.tar.gz 6565857 BLAKE2B e18bd45c9422b97e129418804bb063806614a707dbb9bafd42ae77a0899328cbade45a3b9d8a91f6a07e3508b6b8b3e4b964ee0c9b838a0d6d9cd5eef04d83f6 SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b
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
-}