[Debian-med-packaging] [SCM] igv branch, master, updated. c6a4cc6552e8121d500bce37dba9b00a84e2d9b2

Shaun Jackman sjackman at debian.org
Fri Jul 2 22:19:41 UTC 2010


The following commit has been merged in the master branch:
commit c6a4cc6552e8121d500bce37dba9b00a84e2d9b2
Author: Shaun Jackman <sjackman at debian.org>
Date:   Fri Jul 2 15:12:30 2010 -0700

    Package IGV 1.5.01. Add get-orig-source to debian/rules.

diff --git a/debian/README.source b/debian/README.source
index fbef6f0..6ffcbda 100644
--- a/debian/README.source
+++ b/debian/README.source
@@ -1,4 +1,4 @@
-Binary files in native/ and unused JAR files in lib/ have been removed
-from the original upstream source.
+Binary files in native/ and unneeded JAR files in lib/ have been
+removed from the original upstream source.
 
- -- Shaun Jackman <sjackman at debian.org> 2010-06-24
+ -- Shaun Jackman <sjackman at debian.org> 2010-07-02
diff --git a/debian/changelog b/debian/changelog
index e2d6f24..da8983e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+igv (1.5.01-1) UNRELEASED; urgency=low
+
+  * New upstream release. 
+
+ -- Shaun Jackman <sjackman at debian.org>  Fri, 02 Jul 2010 10:26:19 -0700
+
 igv (1.4.2-1) UNRELEASED; urgency=low
 
   * Initial release. Closes: #585457.
diff --git a/debian/control b/debian/control
index c577912..465a150 100644
--- a/debian/control
+++ b/debian/control
@@ -4,21 +4,21 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Shaun Jackman <sjackman at debian.org>
-Build-Depends: ant, openjdk-6-jdk, debhelper (>= 7.0.50~),
- junit4, libcommons-math-java, libconcurrent-java, libjargs-java,
- libjhdf5-java, libjlibeps-java, liblog4j1.2-java, libsam-java,
- libswing-layout-java
-Standards-Version: 3.8.4
+Build-Depends: ant, junit4, openjdk-6-jdk|java-compiler, debhelper (>= 7.0.50~),
+ libbatik-java, 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
+Standards-Version: 3.9.0.0
 Homepage: http://www.broadinstitute.org/igv/
 Vcs-Git: git://git.debian.org/git/debian-med/igv.git
 Vcs-Browser: http://git.debian.org/?p=debian-med/igv.git
 
 Package: igv
 Architecture: any
-Depends: openjdk-6-jre, ${shlibs:Depends}, ${misc:Depends},
- junit4, libcommons-math-java, libconcurrent-java, libjargs-java,
- libjhdf5-java, libjlibeps-java, liblog4j1.2-java, libsam-java,
- libswing-layout-java
+Depends: openjdk-6-jre|java-runtime, ${shlibs:Depends}, ${misc:Depends},
+ libbatik-java, libcommons-math-java, libcommons-net-java, libconcurrent-java,
+ libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java, liblog4j1.2-java,
+ libsam-java, libswing-layout-java, libxml-commons-external-java
 Description: Integrative Genomics Viewer
  The Integrative Genomics Viewer (IGV) is a high-performance
  visualization tool for interactive exploration of large, integrated
diff --git a/debian/igv.1 b/debian/igv.1
index 376a494..bb6aba0 100644
--- a/debian/igv.1
+++ b/debian/igv.1
@@ -1,4 +1,4 @@
-.TH IGV "1" "June 2010" "IGV 1.4.2" "User Commands"
+.TH IGV "1" "July 2010" "IGV 1.5" "User Commands"
 .SH NAME
 igv \- Integrative Genomics Viewer
 .SH SYNOPSIS
diff --git a/debian/patches/debian-changes-1.4.2-1 b/debian/patches/debian-changes-1.4.2-1
deleted file mode 100644
index 88044ed..0000000
--- a/debian/patches/debian-changes-1.4.2-1
+++ /dev/null
@@ -1,171 +0,0 @@
---- igv-1.4.2.orig/build.xml
-+++ igv-1.4.2/build.xml
-@@ -6,7 +6,7 @@
- 
-     <!-- Source and lib directories -->
-     <property name="src.dir"       value="${basedir}/src/" />
--    <property name="lib.dir"       value="${basedir}/lib/" />
-+    <property name="lib.dir"       value="/usr/share/java/" />
- 
-     <!-- Platform specific input files -->
-     <property name="native.dir"        value="${basedir}/native/" />
-@@ -49,36 +49,26 @@
-                 <exclude name="**/manifest.mf"/>
-             </fileset>
-         </copy>
-+        <unjar dest="${tmp.dir}">
-+            <fileset dir="lib"/>
-+        </unjar>
- 
- 
-         <!-- Create class path for manifest -->
-         <path id="@jars">
--            <pathelement path="${lib.dir}AbsoluteLayout.jar" />
--            <pathelement path="${lib.dir}ATV-3.1.jar" />
--            <pathelement path="${lib.dir}colt.jar" />
--            <pathelement path="${lib.dir}commons-math-1.1.jar" />
-+            <pathelement path="${lib.dir}commons-math.jar" />
-             <pathelement path="${lib.dir}concurrent.jar" />
-             <pathelement path="${lib.dir}jargs.jar" />
-             <pathelement path="${lib.dir}jhdf5.jar" />
--            <pathelement path="${lib.dir}jhdf.jar" />
--            <pathelement path="${lib.dir}jibble.jar" />
--            <pathelement path="${lib.dir}jide-action.jar" />
--            <pathelement path="${lib.dir}jide-common.jar" />
--            <pathelement path="${lib.dir}jide-components.jar" />
--            <pathelement path="${lib.dir}jide-dialogs.jar" />
--            <pathelement path="${lib.dir}jide-dock.jar" />
--            <pathelement path="${lib.dir}jide-grids.jar" />
--            <pathelement path="${lib.dir}junit-4.5.jar" />
--            <pathelement path="${lib.dir}jlfgr-1_0.jar" />
--            <pathelement path="${lib.dir}ledatastream.jar" />
--            <pathelement path="${lib.dir}log4j-1.2.15.jar" />
--            <pathelement path="${lib.dir}maf.jar" />
--            <pathelement path="${lib.dir}sam-1.08.jar" />
--            <pathelement path="${lib.dir}swing-layout-1.0.jar" />
-+            <pathelement path="${lib.dir}net.sourceforge.jlibeps.jar" />
-+            <pathelement path="${lib.dir}junit4.jar" />
-+            <pathelement path="${lib.dir}log4j-1.2.jar" />
-+            <pathelement path="${lib.dir}sam.jar" />
-+            <pathelement path="${lib.dir}swing-layout.jar" />
-         </path>
- 
-         <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
--            <map from="${lib.dir}" to="lib/"/>
-+            <map from="${lib.dir}" to=""/>
-         </pathconvert>
- 
-         <tstamp>
-@@ -94,8 +84,8 @@
-     </target>
- 
-     <target name="build" depends="compile">
--        <jar destfile="${basedir}/${jar.name}"  basedir="${tmp.dir}">
--
-+        <jar destfile="${basedir}/${jar.name}"  basedir="${tmp.dir}" index="true">
-+			<indexjars refid="@jars" />
-             <manifest>
-             <attribute name="Class-Path" value="${class-path}" />
-             <attribute name="Built-By" value="${user.name}" />
-@@ -105,8 +95,13 @@
-     </target>
- 
-     <target name="compile" depends="init">
--        <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
-+        <javac srcdir="${src.dir}" excludes="org/broad/igv/maf/*" debug="on" destdir="${tmp.dir}">
-             <classpath refid="@jars" />
-+            <classpath>
-+                <fileset dir="lib">
-+                    <include name="**/*.jar"/>
-+                </fileset>
-+            </classpath>
-         </javac>
-     </target>
- 
---- igv-1.4.2.orig/src/org/broad/igv/PreferenceManager.java
-+++ igv-1.4.2/src/org/broad/igv/PreferenceManager.java
-@@ -25,7 +25,9 @@
- 
- import org.apache.log4j.Logger;
- import org.broad.igv.feature.Mutation;
-+/*
- import org.broad.igv.maf.MAFManager;
-+*/
- import org.broad.igv.renderer.ColorScaleFactory;
- import org.broad.igv.renderer.ContinuousColorScale;
- import org.broad.igv.track.TrackType;
-@@ -305,7 +307,9 @@
- 
-         String[] species = null;
-         if (tmp == null) {
-+/*
-             species = MAFManager.species;
-+*/
-         } else {
-             species = tmp.split(":");
-         }
---- igv-1.4.2.orig/src/org/broad/igv/h5/HDF5LocalWriter.java
-+++ igv-1.4.2/src/org/broad/igv/h5/HDF5LocalWriter.java
-@@ -491,7 +491,7 @@
-                 buf =
-                         new double[]{((Number) value).doubleValue()};
-             } else {
--                dataType = H5.H5Tcopy(H5.J2C(HDF5Constants.H5T_C_S1));
-+                dataType = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
-                 buf =
-                         value.toString().getBytes();
-                 H5.H5Tset_size(dataType, ((byte[]) buf).length);
---- igv-1.4.2.orig/src/org/broad/igv/track/TrackManager.java
-+++ igv-1.4.2/src/org/broad/igv/track/TrackManager.java
-@@ -34,9 +34,11 @@
- import org.broad.igv.exceptions.DataLoadException;
- import org.broad.igv.feature.*;
- import org.broad.igv.feature.dranger.DRangerParser;
-+/*
- import org.broad.igv.maf.MAFTrack;
- import org.broad.igv.maf.conservation.OmegaDataSource;
- import org.broad.igv.maf.conservation.OmegaTrack;
-+*/
- import org.broad.igv.renderer.DASFeatureRenderer;
- import org.broad.igv.renderer.GeneTrackRenderer;
- import org.broad.igv.renderer.HeatmapRenderer;
-@@ -820,10 +822,12 @@
-                     typeString.endsWith(".aligned") || typeString.endsWith(".sai") ||
-                     typeString.endsWith(".bai") || typeString.endsWith(".bedz")) {
-                 loadAlignmentsTrack(locator, newTracks);
-+/*
-             } else if (typeString.endsWith(".maf")) {
-                 loadMAFTrack(locator, newTracks);
-             } else if (typeString.endsWith("omega")) {
-                 loadOmegaTrack(locator, newTracks);
-+*/
-             } else if (typeString.endsWith("wig")) {
-                 loadWigFile(locator, newTracks);
-             } else if (typeString.endsWith("list")) {
-@@ -1299,6 +1303,7 @@
-         (new RNAIHairpinParser(locator.getPath())).parse();
-     }
- 
-+/*
-     private void loadMAFTrack(ResourceLocator locator, List<Track> newTracks) {
- 
-         MAFTrack t = new MAFTrack(locator, "Multiple Alignments");
-@@ -1315,6 +1320,7 @@
-         //track.setDataRange(new DataRange(-3, 0, 3));
-         newTracks.add(track);
-     }
-+*/
- 
-     /**
-      * Load a rnai gene score file and create a datasource and track.
---- igv-1.4.2.orig/src/org/broad/igv/ui/util/GenericUtilities.java
-+++ igv-1.4.2/src/org/broad/igv/ui/util/GenericUtilities.java
-@@ -27,7 +27,7 @@
- 
- import org.apache.log4j.Logger;
- import org.broad.igv.IGVConstants;
--import org.jibble.epsgraphics.EpsGraphics2D;
-+import org.sourceforge.jlibeps.epsgraphics.*;
- 
- import javax.imageio.ImageIO;
- import javax.swing.filechooser.FileFilter;
diff --git a/debian/patches/debian-changes-1.5.01-1 b/debian/patches/debian-changes-1.5.01-1
new file mode 100644
index 0000000..620c198
--- /dev/null
+++ b/debian/patches/debian-changes-1.5.01-1
@@ -0,0 +1,130 @@
+Description: Upstream changes introduced in version 1.5.01-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ igv (1.5.01-1) UNRELEASED; urgency=low
+ .
+   * New upstream release.
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Shaun Jackman <sjackman at debian.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+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>
+
+--- igv-1.5.01.orig/build.xml
++++ igv-1.5.01/build.xml
+@@ -24,7 +24,7 @@
+ 
+     <!-- Source and lib directories -->
+     <property name="src.dir"       value="${basedir}/src/" />
+-    <property name="lib.dir"       value="${basedir}/lib/" />
++    <property name="lib.dir"       value="/usr/share/java/" />
+ 
+     <!-- Platform specific input files -->
+     <property name="native.dir"        value="${basedir}/native/" />
+@@ -67,49 +67,41 @@
+                 <exclude name="**/manifest.mf"/>
+             </fileset>
+         </copy>
+-
++        <unjar dest="${tmp.dir}">
++            <fileset dir="lib" />
++        </unjar>
+ 
+         <!-- Create class path for manifest -->
+         <path id="@jars">
+-            <pathelement path="${lib.dir}AbsoluteLayout.jar" />
+-            <pathelement path="${lib.dir}batik-awt-util.jar" />
++			<pathelement path="${lib.dir}batik-awt-util.jar" />
+ 			<pathelement path="${lib.dir}batik-css.jar" />
+-            <pathelement path="${lib.dir}batik-dom.jar" />
+-            <pathelement path="${lib.dir}batik-ext.jar" />
++			<pathelement path="${lib.dir}batik-dom.jar" />
++			<pathelement path="${lib.dir}batik-ext.jar" />
+ 			<pathelement path="${lib.dir}batik-gui-util.jar" />
+ 			<pathelement path="${lib.dir}batik-gvt.jar" />
+ 			<pathelement path="${lib.dir}batik-parser.jar" />
+ 			<pathelement path="${lib.dir}batik-svg-dom.jar" />
+ 			<pathelement path="${lib.dir}batik-svggen.jar" />
+ 			<pathelement path="${lib.dir}batik-transcoder.jar" />
+-            <pathelement path="${lib.dir}batik-util.jar" />
+-            <pathelement path="${lib.dir}batik-xml.jar" />            
+-            <pathelement path="${lib.dir}colt.jar" />
+-            <pathelement path="${lib.dir}commons-math-1.1.jar" />
+-			<pathelement path="${lib.dir}commons-net-2.0.jar" />
+-            <pathelement path="${lib.dir}concurrent.jar" />
+-            <pathelement path="${lib.dir}jargs.jar" />
+-            <pathelement path="${lib.dir}jhdf5.jar" />
+-            <pathelement path="${lib.dir}jhdf.jar" />
+-            <pathelement path="${lib.dir}jide-action.jar" />
+-            <pathelement path="${lib.dir}jide-common.jar" />
+-            <pathelement path="${lib.dir}jide-components.jar" />
+-            <pathelement path="${lib.dir}jide-dialogs.jar" />
+-            <pathelement path="${lib.dir}jide-dock.jar" />
+-            <pathelement path="${lib.dir}jide-grids.jar" />
+-            <pathelement path="${lib.dir}jlfgr-1_0.jar" />
+-            <pathelement path="${lib.dir}junit-4.5.jar" />            
+-            <pathelement path="${lib.dir}ledatastream.jar" />
+-            <pathelement path="${lib.dir}log4j-1.2.15.jar" />
+-            <pathelement path="${lib.dir}sam-1.21.jar" />
+-            <pathelement path="${lib.dir}swing-layout-1.0.jar" />           
+-            <pathelement path="${lib.dir}xml-apis-ext-1.3.04" />
+-            <pathelement path="${lib.dir}xml-apis-1.3.04.jar" />
+-            <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}commons-math.jar" />
++			<pathelement path="${lib.dir}commons-net.jar" />
++			<pathelement path="${lib.dir}concurrent.jar" />
++			<pathelement path="${lib.dir}jama.jar" />
++			<pathelement path="${lib.dir}jargs.jar" />
++			<pathelement path="${lib.dir}jhdf5.jar" />
++			<pathelement path="${lib.dir}net.sourceforge.jlibeps.jar" />
++			<pathelement path="${lib.dir}junit4.jar" />
++			<pathelement path="${lib.dir}log4j-1.2.jar" />
++			<pathelement path="${lib.dir}sam.jar" />
++			<pathelement path="${lib.dir}swing-layout.jar" />
++			<pathelement path="${lib.dir}xml-apis.jar" />
++			<pathelement path="${lib.dir}xml-apis-ext.jar" />
+         </path>
+ 
+         <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
+-            <map from="${lib.dir}" to="lib/"/>
++            <map from="${lib.dir}" to=""/>
+         </pathconvert>
+ 
+         <tstamp>
+@@ -125,8 +117,8 @@
+     </target>
+ 
+     <target name="build" depends="compile">
+-        <jar destfile="${basedir}/${jar.name}"  basedir="${tmp.dir}">
+-
++        <jar destfile="${basedir}/${jar.name}" basedir="${tmp.dir}" index="true">
++            <indexjars refid="@jars" />
+             <manifest>
+             <attribute name="Class-Path" value="${class-path}" />
+             <attribute name="Built-By" value="${user.name}" />
+@@ -138,6 +130,11 @@
+     <target name="compile" depends="init">
+         <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
+             <classpath refid="@jars" />
++            <classpath>
++                <fileset dir="lib">
++                    <include name="**/*.jar"/>
++                </fileset>
++            </classpath>
+         </javac>
+     </target>
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 45d13b2..6a2c5b8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-debian-changes-1.4.2-1
+debian-changes-1.5.01-1
diff --git a/debian/rules b/debian/rules
index 9ae5268..965211a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,3 +4,14 @@ export DH_OPTIONS
 
 %:
 	dh  $@
+
+v=$(shell dpkg-parsechangelog |sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+get-orig-source:
+	rm -rf igv_$v.orig
+	cd .. && wget -c http://www.broadinstitute.org/igvdata/downloads/IGVDistribution_$v.zip
+	unzip -qo ../IGVDistribution_$v.zip
+	mv IGVDistribution_$v igv_$v.orig
+	rm -rf igv.jar igv_$v.orig/native
+	cd igv_$v.orig/lib && rm -f Jama-* batik* commons-math-* commons-net-* concurrent* jargs* jhdf* log4j-* sam-* swing-layout-* xml-apis-*
+	BZIP2=--best tar cjf ../igv_$v.orig.tar.bz2 igv_$v.orig
+	rm -rf igv_$v.orig

-- 
Integrative Genomics Viewer



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