[Debian-med-packaging] [SCM] picard-tools branch, master, updated. upstream/1.23-11-g115eddf

[Charles Plessy]

The following commit has been merged in the master branch:
commit 115eddf43e41517a2a9e585e2c29d3e92017f8fe
Author: Charles Plessy <plessy at debian.org>
Date:   Sat Jun 26 13:12:29 2010 +0900

    New upstream release 1.24.
    
     - Refreshed debian/patches/debian-changes-1.22-1.
    
     - Create the versionned link to the jar file from debian/rules
       using the $(SRC_VERSION) make variable so that it is not needed
       anymore to refresh debian/links (deleted by this commit).

diff --git a/debian/changelog b/debian/changelog
index 1d9c591..7464363 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-picard-tools (1.23-1) UNRELEASED; urgency=low
+picard-tools (1.24-1) UNRELEASED; urgency=low
 
   * Initial release. Closes: #586015.
 
diff --git a/debian/links b/debian/links
deleted file mode 100644
index 90e48e6..0000000
--- a/debian/links
+++ /dev/null
@@ -1 +0,0 @@
-usr/share/java/sam-1.23.jar usr/share/java/sam.jar
diff --git a/debian/patches/debian-changes-1.22-1 b/debian/patches/debian-changes-1.22-1
index 6eff093..883fe98 100644
--- a/debian/patches/debian-changes-1.22-1
+++ b/debian/patches/debian-changes-1.22-1
@@ -23,6 +23,8 @@ Forwarded: <no|not-needed|url proving that it has been forwarded>
 Reviewed-By: <name and email of someone who approved the patch>
 Last-Update: <YYYY-MM-DD>
 
+Index: picard-tools/build.xml
+===================================================================
 --- picard-tools.orig/build.xml
 +++ picard-tools/build.xml
 @@ -23,7 +23,7 @@
@@ -33,8 +35,8 @@ Last-Update: <YYYY-MM-DD>
 +<project name="picard-public" basedir="." default="sam-jar">
  
      <property name="src" value="src/java"/>
-     <property name="src.test" value="src/tests"/>
-@@ -62,6 +62,7 @@
+     <property name="src.scripts" value="src/scripts"/>
+@@ -63,6 +63,7 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
@@ -42,7 +44,7 @@ Last-Update: <YYYY-MM-DD>
          </path>
      </target>
  
-@@ -92,7 +93,7 @@
+@@ -93,7 +94,7 @@
                 sourcepath="" srcdir="${src}"
                 includes ="net/sf/samtools/**/*.*"
                 excludes = "net/sf/picard/**/*.*"
@@ -51,7 +53,7 @@ Last-Update: <YYYY-MM-DD>
                 compiler="javac1.5" fork="true">
              <!--<compilerarg value="-Xlint:all"/>-->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
-@@ -121,7 +122,7 @@
+@@ -122,7 +123,7 @@
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
                 includes ="net/sf/samtools/**/*.*"
diff --git a/debian/rules b/debian/rules
index 2d8f545..647f22f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -25,3 +25,6 @@ get-orig-source:
 	BZIP2='--best' tar cjf $(TARBALL) -C get-orig-source $(SRC_DIR)
 	rm -r get-orig-source
 	@echo "  "$(TARBALL)" created; move it to the right destination to build the package"
+
+override_dh_link:
+	dh_link	usr/share/java/sam-$(SRC_VERSION).jar usr/share/java/sam.jar

-- 
manipulate SAM and BAM files