debian/bin/igv

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

debian/changelog

@@ -16,17 +16,7 @@ igv (2.4.14+dfsg-1) UNRELEASED; urgency=medium
 
   [ Olivier Sallou]
   * d/patches/fix_gradle.patch: adapt build to Debian
-
-
-  * TODO there is still an issue with batik:
-     - if defined, there are some conflicts
-       (see https://stackoverflow.com/questions/42358084/package-conflicts-with-automatic-modules-in-java-9)
-       where some batik share some package names.
-     - for javafx libs, they are found but marked as not visible.... though
-       should be seen as unnamed modules.
-       javafx libs should be declared as modules with exported packages but
-       needs lib refactoring or we should find a way to put them as "standard"
-       libs and not modules (but how?)
+    Remove java module support as some Debian libs are not modularized yet
 
  -- Andreas Tille <tille@debian.org>  Mon, 01 Oct 2018 21:14:39 +0200
 

debian/igv.jlibs

-igv.jar
+build_java9/libs/igv.jar

debian/log4j.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+<log4j:configuration debug="true"
+	xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+	<appender name="console" class="org.apache.log4j.ConsoleAppender">
+	    <layout class="org.apache.log4j.PatternLayout">
+		<param name="ConversionPattern" 
+		  value="%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n" />
+	    </layout>
+	</appender>
+
+	<logger name="org.broad.igv">
+		<level value="INFO" />
+		<appender-ref ref="console" />
+	</logger>
+
+</log4j:configuration>

debian/patches/fix_gradle.patch

@@ -43,8 +43,8 @@ Forwarded: no
 +    compile files ("/usr/share/maven-repo/org/openjfx/javafx-base/debian/javafx-base-debian-linux.jar")
 +    compile files ("/usr/share/maven-repo/org/openjfx/javafx-swing/debian/javafx-swing-debian-linux.jar")
 +    compile files ("/usr/share/maven-repo/org/openjfx/javafx-fxml/debian/javafx-fxml-debian-linux.jar")
-+    //compile "org.apache.xmlgraphics:batik-dom:debian"
-+    //compile "org.apache.xmlgraphics:batik-svggen:debian"
++    compile "org.apache.xmlgraphics:batik-dom:debian"
++    compile "org.apache.xmlgraphics:batik-svggen:debian"
 +    compile "com.google.guava:guava:debian"
 +    compile "commons-io:commons-io:debian"
 +    compile "org.apache.commons:commons-math:debian"
@@ -62,6 +62,23 @@ Forwarded: no
      testCompile fileTree(dir: 'test/lib', include: '*.jar')
  }
  
+@@ -93,12 +123,13 @@
+ }
+ 
+ compileJava {
+-    inputs.property("moduleName", moduleName)
++    //inputs.property("moduleName", moduleName)
+     doFirst {
+         options.compilerArgs = [
+-            '--module-path', classpath.asPath,
++    //        '--module-path', classpath.asPath,
++              '--add-modules', 'java.xml.bind'
+         ]
+-        classpath = files()
++    //    classpath = files()
+     }
+ }
+ 
 --- a/src/main/java9/module-info.java
 +++ b/src/main/java9/module-info.java
 @@ -93,11 +93,11 @@

debian/rules

@@ -9,6 +9,8 @@ JAVA_HOME=/usr/lib/jvm/default-java
 	dh  $@ --buildsystem=gradle --with javahelper
 
 override_dh_clean:
+	if [ -e src/main/resources/log4j.xml ] ; then rm src/main/resources/log4j.xml ; fi
+	if [ -e src/main/java9/module-info.java.skip ] ; then mv src/main/java9/module-info.java.skip src/main/java9/module-info.java ; fi
 	if [ -e build_java8.gradle ] ; then mv build_java8.gradle build.gradle ; fi
 	rm -f goby-io-igv.jar
 	rm -f batik-codec.jar
@@ -17,3 +19,5 @@ override_dh_clean:
 override_dh_auto_configure:
 	mv build.gradle build_java8.gradle
 	cp -a build_java9.gradle build.gradle
+	mv src/main/java9/module-info.java src/main/java9/module-info.java.skip
+	cp debian/log4j.xml src/main/resources/