[med-svn] [SCM] picard-tools branch, master, updated. debian/1.90-3-7-g53b7a12

[Olivier Sallou]

The following commit has been merged in the master branch:
commit c332c8f4574bf4305e635289d7309d96c30d5a74
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Thu Jul 25 13:38:33 2013 +0200

    update patches for new release

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index ffa30a1..d462572 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -16,16 +16,7 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -51,7 +51,7 @@
-     <property name="command_tmp" value=".command_tmp"/>
-     <property name="command-line-html-dir" value="${dist}/html"/>
-     <property name="testng.verbosity" value="2"/>
--    <property name="contracts.jar" value="${lib}/cofoja-1.0-r139.jar"/>
-+    <property name="contracts.jar" value="/usr/share/java/cofoja.jar"/>
- 
-     <property environment="env"/>
- 
-@@ -72,6 +72,11 @@
+@@ -70,6 +70,11 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
@@ -37,16 +28,15 @@ Forwarded: no
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -209,7 +214,7 @@
-         <mkdir dir="${dist}"/>
+@@ -195,7 +200,6 @@
          <jar destfile="${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"/>
-+            <fileset dir="${src.scripts}" includes="**/*.R"/>
              <manifest>
                  <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
                  <attribute name="Implementation-Vendor" value="Broad Institute"/>
-@@ -239,6 +244,8 @@
+@@ -225,6 +229,8 @@
          </copy>
      </target>
  

-- 
manipulate SAM and BAM files