[Debian-med-packaging] [SCM] igv branch, master, updated. 1a23031f99654381c8a6d0b53a1f48d3f9c36735

[Shaun Jackman]

The following commit has been merged in the master branch:
commit f5c150e01900fc130834ca7ca0ac3917d80cc2e2
Author: Shaun Jackman <sjackman at debian.org>
Date:   Fri Jun 25 14:57:51 2010 -0700

    * build.xml: Index the JAR file.
    * debian/bin/igv: Use java -jar.
    * debian/igv.1: Mention java -jar in the synopsis.

diff --git a/debian/bin/igv b/debian/bin/igv
index c8373bf..13e4b2a 100755
--- a/debian/bin/igv
+++ b/debian/bin/igv
@@ -1,5 +1,3 @@
 #!/bin/sh
 set -eu
-p=/usr/share/java
-exec java -classpath "$p/igv.jar:$p/commons-math.jar:$p/concurrent.jar:$p/jargs.jar:$p/jhdf5.jar:$p/net.sourceforge.jlibeps.jar:$p/junit4.jar:$p/log4j-1.2.jar:$p/sam.jar:$p/swing-layout.jar" \
-	org.broad.igv.ui.IGVMainFrame "$@"
+exec java -jar /usr/share/java/igv.jar "$@"
diff --git a/debian/igv.1 b/debian/igv.1
index b86b038..376a494 100644
--- a/debian/igv.1
+++ b/debian/igv.1
@@ -3,6 +3,10 @@
 igv \- Integrative Genomics Viewer
 .SH SYNOPSIS
 .B igv
+.br
+or
+.br
+\fBjava\fR -jar /usr/share/java/igv.jar
 .SH DESCRIPTION
 The Integrative Genomics Viewer (IGV) is a high-performance
 visualization tool for interactive exploration of large, integrated
diff --git a/debian/patches/debian-changes-1.4.2-1 b/debian/patches/debian-changes-1.4.2-1
index 9e52818..d61cf69 100644
--- a/debian/patches/debian-changes-1.4.2-1
+++ b/debian/patches/debian-changes-1.4.2-1
@@ -9,7 +9,7 @@
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -49,36 +49,25 @@
+@@ -49,36 +49,26 @@
                  <exclude name="**/manifest.mf"/>
              </fileset>
          </copy>
@@ -52,10 +52,22 @@
  
          <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
 -            <map from="${lib.dir}" to="lib/"/>
++            <map from="${lib.dir}" to=""/>
          </pathconvert>
  
          <tstamp>
-@@ -105,8 +94,13 @@
+@@ -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">
@@ -72,7 +84,7 @@
  
 --- 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 @@ package org.broad.igv;
+@@ -25,7 +25,9 @@
  
  import org.apache.log4j.Logger;
  import org.broad.igv.feature.Mutation;
@@ -82,7 +94,7 @@
  import org.broad.igv.renderer.ColorScaleFactory;
  import org.broad.igv.renderer.ContinuousColorScale;
  import org.broad.igv.track.TrackType;
-@@ -305,7 +307,9 @@ public class PreferenceManager implement
+@@ -305,7 +307,9 @@
  
          String[] species = null;
          if (tmp == null) {
@@ -94,7 +106,7 @@
          }
 --- 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 @@ public class HDF5LocalWriter implements 
+@@ -491,7 +491,7 @@
                  buf =
                          new double[]{((Number) value).doubleValue()};
              } else {
@@ -105,7 +117,7 @@
                  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.data.rnai.RNAIHairp
+@@ -34,9 +34,11 @@
  import org.broad.igv.exceptions.DataLoadException;
  import org.broad.igv.feature.*;
  import org.broad.igv.feature.dranger.DRangerParser;
@@ -117,7 +129,7 @@
  import org.broad.igv.renderer.DASFeatureRenderer;
  import org.broad.igv.renderer.GeneTrackRenderer;
  import org.broad.igv.renderer.HeatmapRenderer;
-@@ -820,10 +822,12 @@ public class TrackManager {
+@@ -820,10 +822,12 @@
                      typeString.endsWith(".aligned") || typeString.endsWith(".sai") ||
                      typeString.endsWith(".bai") || typeString.endsWith(".bedz")) {
                  loadAlignmentsTrack(locator, newTracks);
@@ -130,7 +142,7 @@
              } else if (typeString.endsWith("wig")) {
                  loadWigFile(locator, newTracks);
              } else if (typeString.endsWith("list")) {
-@@ -1299,6 +1303,7 @@ public class TrackManager {
+@@ -1299,6 +1303,7 @@
          (new RNAIHairpinParser(locator.getPath())).parse();
      }
  
@@ -138,7 +150,7 @@
      private void loadMAFTrack(ResourceLocator locator, List<Track> newTracks) {
  
          MAFTrack t = new MAFTrack(locator, "Multiple Alignments");
-@@ -1315,6 +1320,7 @@ public class TrackManager {
+@@ -1315,6 +1320,7 @@
          //track.setDataRange(new DataRange(-3, 0, 3));
          newTracks.add(track);
      }
@@ -148,7 +160,7 @@
       * 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 @@ package org.broad.igv.ui.util;
+@@ -27,7 +27,7 @@
  
  import org.apache.log4j.Logger;
  import org.broad.igv.IGVConstants;

-- 
Integrative Genomics Viewer