debian/bin/igv

 #!/bin/sh
 set -eu
 
-exec java -cp /usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
+exec java -cp /usr/share/java/ant.jar:/usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
 

debian/changelog

-igv (2.4.16+dfsg-1) UNRELEASED; urgency=medium
+igv (2.4.16+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Drop Build-Depends: libmysql-java, Recommends: libmariadb-java

debian/control

@@ -39,7 +39,8 @@ Build-Depends: default-jdk,
                libjide-oss-java,
                libfest-assert-java,
                libfest-util-java,
-               libfest-reflect-java
+               libfest-reflect-java,
+               ant
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/igv
 Vcs-Git: https://salsa.debian.org/med-team/igv.git

debian/patches/fix_gradle.patch

@@ -5,7 +5,7 @@ Description: gradle build file needs to add debian based libraries
  case, system tries to get it from Jar name, so module names need also to be
  adapted for those libraries to match Debian jar names.
 Author: Olivier Sallou <osallou@debian.org>
-Last-Updated: 2018-10-15
+Last-Updated: 2018-10-17
 Forwarded: no
 --- a/build_java9.gradle
 +++ b/build_java9.gradle
@@ -21,7 +21,7 @@ Forwarded: no
  import org.apache.tools.ant.filters.ReplaceTokens
  
  ext.moduleName = 'org.igv'
-@@ -30,6 +33,12 @@ ext.mainClassName = 'org.broad.igv.ui.Ma
+@@ -30,6 +33,12 @@
  // Despite this, it is recommended that Java 8 vs. 9 builds be run in different locations.
  buildDir = 'build_java9' 
  
@@ -34,7 +34,7 @@ Forwarded: no
  sourceSets {
      main {
          java {
-@@ -45,6 +54,28 @@ sourceSets {
+@@ -45,6 +54,29 @@
  dependencies {
      // Use the newer JIDE lib for Java 9 builds
      compile fileTree(dir: 'lib', include: '*.jar', exclude: 'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')
@@ -60,10 +60,11 @@ Forwarded: no
 +    compile "org.apache.logging.log4j:log4j-core:debian"
 +    compile "org.swinglabs:swing-layout:debian"
 +    compile "com.github.samtools:htsjdk:debian"
++    compile "org.apache.ant:ant:debian"
      testCompile fileTree(dir: 'test/lib', include: '*.jar')
  }
  
-@@ -52,8 +83,8 @@ task wrapper(type: Wrapper) {
+@@ -52,8 +84,8 @@
      gradleVersion = '4.4.1'
  }
  
@@ -74,7 +75,7 @@ Forwarded: no
  
  processResources {
      // Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
-@@ -93,12 +124,9 @@ task tooljar(type: Jar, dependsOn: jar)
+@@ -93,12 +125,9 @@
  }
  
  compileJava {
@@ -91,7 +92,7 @@ Forwarded: no
  
 --- a/src/main/java9/module-info.java
 +++ b/src/main/java9/module-info.java
-@@ -5,11 +5,11 @@ module org.igv {
+@@ -5,11 +5,11 @@
      
      requires AbsoluteLayout;
      requires ant;
@@ -107,7 +108,7 @@ Forwarded: no
      requires htsjdk;
      requires java.datatransfer;
      requires java.desktop;
-@@ -22,5 +22,5 @@ module org.igv {
+@@ -22,5 +22,5 @@
      requires log4j;
      requires org.apache.logging.log4j;
      requires org.apache.logging.log4j.core;
@@ -116,7 +117,7 @@ Forwarded: no
  }
 --- a/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
 +++ b/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
-@@ -87,16 +87,6 @@ public class IGVSeekableBufferedStream e
+@@ -87,16 +87,6 @@
          return actualSkip;
      }
  
@@ -133,7 +134,7 @@ Forwarded: no
      public void seek(final long position) throws IOException {
          this.position = position;
      }
-@@ -215,4 +205,4 @@ public class IGVSeekableBufferedStream e
+@@ -215,4 +205,4 @@
              bufferSize = tmpBufferSize;
          }
      }