diff options
Diffstat (limited to 'sci-biology/picard/files/1.103-gentoo.patch')
| -rw-r--r-- | sci-biology/picard/files/1.103-gentoo.patch | 131 |
1 files changed, 131 insertions, 0 deletions
diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch new file mode 100644 index 000000000000..00e89b95056a --- /dev/null +++ b/sci-biology/picard/files/1.103-gentoo.patch @@ -0,0 +1,131 @@ +diff --git a/build.xml b/build.xml +index fca2271..11f4fbd 100755 +--- a/build.xml ++++ b/build.xml +@@ -52,9 +52,6 @@ + <property name="testng.verbosity" value="2"/> + <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> + +- <property environment="env"/> +- <property name="java6.home" value="${env.JAVA6_HOME}"/> +- + <condition property="isUnix"> + <os family="unix"/> + </condition> +@@ -78,9 +75,6 @@ + <pathelement location="${classes}"/> + </path> + +- <path id="java6.lib.ref"> +- <fileset dir="${java6.home}/lib" includes="*.jar"/> +- </path> + </target> + + <!-- CLEAN --> +@@ -94,10 +88,6 @@ + </target> + + <!-- COMPILE --> +- <target name="compile" depends="compile-src, compile-tests" +- description="Compile files without cleaning"> +- </target> +- + <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> + + <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> +@@ -138,7 +128,7 @@ + </target> + + <!-- TEST --> +- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> ++ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> + <taskdef resource="testngtasks" classpathref="classpath"/> + <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" + failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" +@@ -151,6 +141,8 @@ + <classfileset dir="${classes.test}"> + <include name="**/Test*.class"/> + <include name="**/*Test.class"/> ++ <exclude name="**/ValidateSamFileTest.class" /> ++ <exclude name="**/VCFWriterUnitTest.class" /> + </classfileset> + <jvmarg value="-Xmx2G"/> + </testng> +@@ -165,7 +157,7 @@ + </target> + + <target name="single-test" +- depends="compile, compile-tests" ++ depends="compile-tests" + description="Compile and run a single test."> + <taskdef resource="testngtasks" classpathref="classpath"/> + <fail unless="name" message="Please provide input test: -Dname=..." /> +@@ -200,13 +192,12 @@ + </jar> + </target> + +- <target name="picard-jar" depends="compile" ++ <target name="picard-jar" depends="compile-src" + description="Builds picard-${picard-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> + <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> + <fileset dir="${src.scripts}" includes="**/*.R"/> +- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> + <manifest> + <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> + <attribute name="Implementation-Vendor" value="Broad Institute"/> +@@ -214,7 +205,7 @@ + </jar> + </target> + +- <target name="tribble-jar" depends="compile" ++ <target name="tribble-jar" depends="compile-src" + description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> +@@ -225,7 +216,7 @@ + </copy> + </target> + +- <target name="variant-jar" depends="compile" ++ <target name="variant-jar" depends="compile-src" + description="Builds variant-${variant-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> +@@ -262,7 +253,7 @@ + </javadoc> + </target> + +- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> ++ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> + <delete dir="${command_tmp}"/> + + <mkdir dir="${command_tmp}"/> +@@ -344,7 +335,7 @@ + </target> + + <!-- ALL --> +- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> ++ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> + <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> + <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> + <zipfileset dir="${lib}" includes="snappy*.jar"/> +@@ -468,8 +459,6 @@ + target="${javac.target}"> + <classpath refid="@{compile.classpath}"/> + <compilerarg line="@{compiler.args}" /> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> +@@ -494,8 +483,6 @@ + <pathelement location="${classes}"/> + </classpath> + <compilerarg line="@{compiler.args}"/> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> |