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ercpe 13/11/24 15:21:14 |
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Added: 1.103-gentoo.patch |
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Log: |
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Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements (wrt #491816) |
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(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key 77C501ED) |
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Revision Changes Path |
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1.1 sci-biology/picard/files/1.103-gentoo.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/files/1.103-gentoo.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/files/1.103-gentoo.patch?rev=1.1&content-type=text/plain |
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Index: 1.103-gentoo.patch |
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=================================================================== |
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diff --git a/build.xml b/build.xml |
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index fca2271..11f4fbd 100755 |
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--- a/build.xml |
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+++ b/build.xml |
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@@ -52,9 +52,6 @@ |
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<property name="testng.verbosity" value="2"/> |
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<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> |
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|
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- <property environment="env"/> |
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- <property name="java6.home" value="${env.JAVA6_HOME}"/> |
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- |
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<condition property="isUnix"> |
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<os family="unix"/> |
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</condition> |
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@@ -78,9 +75,6 @@ |
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<pathelement location="${classes}"/> |
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</path> |
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|
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- <path id="java6.lib.ref"> |
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- <fileset dir="${java6.home}/lib" includes="*.jar"/> |
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- </path> |
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</target> |
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|
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<!-- CLEAN --> |
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@@ -94,10 +88,6 @@ |
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</target> |
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|
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<!-- COMPILE --> |
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- <target name="compile" depends="compile-src, compile-tests" |
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- description="Compile files without cleaning"> |
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- </target> |
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- |
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<target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> |
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|
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<target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> |
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@@ -138,7 +128,7 @@ |
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</target> |
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|
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<!-- TEST --> |
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- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> |
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+ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> |
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<taskdef resource="testngtasks" classpathref="classpath"/> |
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<testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" |
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failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" |
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@@ -151,6 +141,8 @@ |
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<classfileset dir="${classes.test}"> |
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<include name="**/Test*.class"/> |
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<include name="**/*Test.class"/> |
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+ <exclude name="**/ValidateSamFileTest.class" /> |
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+ <exclude name="**/VCFWriterUnitTest.class" /> |
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</classfileset> |
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<jvmarg value="-Xmx2G"/> |
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</testng> |
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@@ -165,7 +157,7 @@ |
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</target> |
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|
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<target name="single-test" |
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- depends="compile, compile-tests" |
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+ depends="compile-tests" |
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description="Compile and run a single test."> |
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<taskdef resource="testngtasks" classpathref="classpath"/> |
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<fail unless="name" message="Please provide input test: -Dname=..." /> |
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@@ -200,13 +192,12 @@ |
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</jar> |
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</target> |
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|
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- <target name="picard-jar" depends="compile" |
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+ <target name="picard-jar" depends="compile-src" |
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description="Builds picard-${picard-version}.jar for inclusion in other projects"> |
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<mkdir dir="${dist}"/> |
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<jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> |
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<fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> |
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<fileset dir="${src.scripts}" includes="**/*.R"/> |
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- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> |
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<manifest> |
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<attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> |
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<attribute name="Implementation-Vendor" value="Broad Institute"/> |
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@@ -214,7 +205,7 @@ |
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</jar> |
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</target> |
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|
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- <target name="tribble-jar" depends="compile" |
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+ <target name="tribble-jar" depends="compile-src" |
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description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> |
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<mkdir dir="${dist}"/> |
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<jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> |
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@@ -225,7 +216,7 @@ |
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</copy> |
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</target> |
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|
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- <target name="variant-jar" depends="compile" |
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+ <target name="variant-jar" depends="compile-src" |
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description="Builds variant-${variant-version}.jar for inclusion in other projects"> |
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<mkdir dir="${dist}"/> |
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<jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> |
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@@ -262,7 +253,7 @@ |
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</javadoc> |
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</target> |
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|
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- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> |
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+ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> |
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<delete dir="${command_tmp}"/> |
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|
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<mkdir dir="${command_tmp}"/> |
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@@ -344,7 +335,7 @@ |
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</target> |
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<!-- ALL --> |
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- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> |
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+ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> |
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<zip zipfile="${dist}/picard-tools-${picard-version}.zip"> |
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<zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> |
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<zipfileset dir="${lib}" includes="snappy*.jar"/> |
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@@ -468,8 +459,6 @@ |
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target="${javac.target}"> |
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<classpath refid="@{compile.classpath}"/> |
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<compilerarg line="@{compiler.args}" /> |
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- <!-- ensure that Java 6 bootclasspath is used --> |
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- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> |
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</javac> |
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</sequential> |
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</macrodef> |
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@@ -494,8 +483,6 @@ |
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<pathelement location="${classes}"/> |
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</classpath> |
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<compilerarg line="@{compiler.args}"/> |
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- <!-- ensure that Java 6 bootclasspath is used --> |
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- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> |
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</javac> |
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</sequential> |
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</macrodef> |
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