[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.5.03-33-g80bd695

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 80bd695c0a241c38c4c3c6f992476fdf52145e82
Author: Shaun Jackman <sjackman at debian.org>
Date:   Wed Jul 14 11:33:05 2010 -0700

    * New upstream release.
    * debian/control (Build-Depends, Depends): Add libcolt-java.
    * debian/rules (get-orig-source): Remove lib/colt.jar.
    * debian/patches/01-build.xml: Refresh.

diff --git a/debian/changelog b/debian/changelog
index b796424..10630b0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+igv (1.5.06-1) unstable; urgency=low
+
+  * New upstream release.
+  * Depend on libcolt-java.
+
+ -- Shaun Jackman <sjackman at debian.org>  Wed, 14 Jul 2010 11:31:22 -0700
+
 igv (1.5.05-1) UNRELEASED; urgency=low
 
   * New upstream release.
diff --git a/debian/control b/debian/control
index 4a39385..89f4da7 100644
--- a/debian/control
+++ b/debian/control
@@ -5,9 +5,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 DM-Upload-Allowed: yes
 Uploaders: Shaun Jackman <sjackman at debian.org>
 Build-Depends: ant, junit4, openjdk-6-jdk|java-compiler, debhelper (>= 7.0.50~),
- libbatik-java (>>1.7), libcommons-math-java, libcommons-net-java, libconcurrent-java,
- libjlibeps-java, libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java, liblog4j1.2-java,
- libsam-java, libswing-layout-java, libxml-commons-external-java
+ libbatik-java (>>1.7), libcolt-java,
+ libcommons-math-java, libcommons-net-java, libconcurrent-java,
+ libjlibeps-java, libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java,
+ liblog4j1.2-java, libsam-java, libswing-layout-java,
+ libxml-commons-external-java
 Standards-Version: 3.9.0
 Homepage: http://www.broadinstitute.org/igv/
 Vcs-Git: git://git.debian.org/git/debian-med/igv.git
@@ -16,9 +18,11 @@ Vcs-Browser: http://git.debian.org/?p=debian-med/igv.git
 Package: igv
 Architecture: all
 Depends: openjdk-6-jre|java-runtime, ${shlibs:Depends}, ${misc:Depends},
- libbatik-java (>>1.7), libcommons-math-java, libcommons-net-java, libconcurrent-java,
- libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java, liblog4j1.2-java,
- libsam-java, libswing-layout-java, libxml-commons-external-java
+ libbatik-java (>>1.7), libcolt-java,
+ libcommons-math-java, libcommons-net-java, libconcurrent-java,
+ libjlibeps-java, libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java,
+ liblog4j1.2-java, libsam-java, libswing-layout-java,
+ libxml-commons-external-java
 Description: Integrative Genomics Viewer
  The Integrative Genomics Viewer (IGV) is a high-performance
  visualization tool for interactive exploration of large, integrated
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index aa761a8..8c1a6ee 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -12,7 +12,7 @@ Forwarded: no
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -67,51 +67,41 @@
+@@ -67,51 +67,42 @@
                  <exclude name="**/manifest.mf"/>
              </fileset>
          </copy>
@@ -65,6 +65,7 @@ Forwarded: no
 -            <pathelement path="${lib.dir}Jama-1.0.2.jar" />
 +			<pathelement path="${lib.dir}batik-util.jar" />
 +			<pathelement path="${lib.dir}batik-xml.jar" />
++			<pathelement path="${lib.dir}colt.jar" />
 +			<pathelement path="${lib.dir}commons-math.jar" />
 +			<pathelement path="${lib.dir}commons-net.jar" />
 +			<pathelement path="${lib.dir}concurrent.jar" />
@@ -86,7 +87,7 @@ Forwarded: no
          </pathconvert>
  
          <tstamp>
-@@ -127,8 +117,8 @@
+@@ -127,8 +118,8 @@
      </target>
  
      <target name="build" depends="compile">
@@ -97,7 +98,7 @@ Forwarded: no
              <manifest>
              <attribute name="Class-Path" value="${class-path}" />
              <attribute name="Built-By" value="${user.name}" />
-@@ -140,6 +130,11 @@
+@@ -140,6 +131,11 @@
      <target name="compile" depends="init">
          <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
              <classpath refid="@jars" />
diff --git a/debian/rules b/debian/rules
index 024aebc..5c34f22 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,6 +12,6 @@ get-orig-source:
 	unzip -qo ../IGVDistribution_$v.zip
 	mv IGVDistribution_$v igv_$v.orig
 	rm -rf igv.jar igv_$v.orig/native
-	cd igv_$v.orig/lib && rm -f Jama-* batik* commons-math-* commons-net-* concurrent* jargs* jhdf* junit-* log4j-* sam-* swing-layout-* xml-apis-*
+	cd igv_$v.orig/lib && rm -f Jama-* batik* colt* commons-math-* commons-net-* concurrent* jargs* jhdf* junit-* log4j-* sam-* swing-layout-* xml-apis-*
 	BZIP2=--best tar cjf ../igv_$v.orig.tar.bz2 igv_$v.orig
 	rm -rf igv_$v.orig

-- 
Integrative Genomics Viewer