The following commit has been merged in the master branch:
commit c04372e540742d5f536dc35387d4801e30387172
Author: Olivier Sallou <[email protected]>
Date: Fri Sep 7 12:02:11 2012 +0200
fix patches for new release
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 66f3a07..76b7ed8 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -24,28 +24,28 @@ Forwarded: no
+ <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/>
+ <pathelement path="/usr/share/java/jbzip2.jar"/>
</path>
- <path id="metrics.classpath">
+ <path id="metrics.classpath">
<pathelement path="${classpath}"/>
-@@ -123,7 +126,8 @@
+@@ -122,7 +125,8 @@
<javac destdir="${classes.test}"
optimize="${javac.opt}"
debug="${javac.debug}"
-- includes="net/sf/samtools/**/*.*">
-+ includes="net/sf/samtools/**/*.*"
+- includes ="net/sf/samtools/**/*.*">
++ includes ="net/sf/samtools/**/*.*"
+ executable="javac">
<!--<compilerarg value="-Xlint:unchecked"/>-->
<src path="${src.test}"/>
<classpath>
-@@ -214,7 +218,7 @@
+@@ -213,7 +217,7 @@
<mkdir dir="${dist}"/>
<jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
- <fileset dir="${classes}" includes="net/sf/picard/**/*.*"/>
+ <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
+ <fileset dir="${src.scripts}" includes="**/*.R"/>
<manifest>
<attribute name="Implementation-Version"
value="${picard-version}(${repository.revision})"/>
<attribute name="Implementation-Vendor" value="Broad
Institute"/>
-@@ -222,6 +226,8 @@
+@@ -221,6 +225,8 @@
</jar>
</target>
--
manipulate SAM and BAM files
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