debian/changelog

@@ -11,6 +11,11 @@ igv (2.4.14+dfsg-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.2.1
   * Upstream switched build system to gradle
 
+  [ Olivier Sallou]
+  * d/patches/fix_gradle.patch: adapt build to Debian
+    // TODO there is still an issue with log4j, Logger class is not found
+       though modules and libraries are loaded in classpath
+
  -- Andreas Tille <tille@debian.org>  Mon, 01 Oct 2018 21:14:39 +0200
 
 igv (2.4.6+dfsg-1) unstable; urgency=medium

debian/patches/fix_gradle.patch

+Subject: adapt gradle build for debian
+Description: gradle build file needs to add debian based libraries
+ Needs some adaptation also to support Java 9 modules.
+ All Debian libraries do not provide Module name in their manifest. In this
+ 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
+Forwarded: no
+--- a/build_java9.gradle
++++ b/build_java9.gradle
+@@ -20,7 +20,10 @@
+ // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ // THE SOFTWARE.
+-apply plugin: 'java'
++plugins {
++ id 'java'
++ id 'maven'
++}
+ import org.apache.tools.ant.filters.ReplaceTokens
+ 
+ ext.moduleName = 'org.broad.igv'
+@@ -30,6 +33,12 @@
+ // Despite this, it is recommended that Java 8 vs. 9 builds be run in different locations.
+ buildDir = 'build_java9' 
+ 
++repositories {
++    mavenCentral()
++    mavenLocal()
++}
++
++
+ sourceSets {
+     main {
+         java {
+@@ -45,6 +54,19 @@
+ 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')
++    compile "com.google.guava:guava:debian"
++    compile "commons-io:commons-io:debian"
++    compile "org.apache.commons:commons-math:debian"
++    compile "com.google.code.gson:gson:debian"
++    compile "org.openjfx:javafx:debian"
++    compile "org.openjfx:javafx-fxml:debian"
++    compile "org.openjfx:javafx-graphics:debian"
++    compile "org.openjfx:javafx-swing:debian"
++    compile "org.jfree:jfreechart:debian"
++    compile "org.apache.logging.log4j:log4j:debian"
++    compile "org.apache.logging.log4j:log4j-api:debian"
++    compile "org.apache.logging.log4j:log4j-core:debian"
++    compile "org.swinglabs:swing-layout:debian"
+     testCompile fileTree(dir: 'test/lib', include: '*.jar')
+ }
+ 
+--- a/src/main/java9/module-info.java
++++ b/src/main/java9/module-info.java
+@@ -93,11 +93,11 @@
+     
+     requires AbsoluteLayout;
+     requires ant;
+-    requires com.google.common;
+-    requires commons.io;
+-    requires commons.math;
++    requires guava.debian;
++    requires org.apache.commons.io;
++    requires commons.math.debian;
+     requires goby.io.igv;
+-    requires gson;
++    requires gson.debian;
+     requires htsjdk;
+     requires java.datatransfer;
+     requires java.desktop;
+@@ -107,15 +107,14 @@
+     requires java.sql;
+     requires java.xml;
+     requires java.xml.bind;
+-    requires javafx.base;
+-    requires javafx.controls;
+-    requires javafx.fxml;
+-    requires javafx.graphics;
+-    requires javafx.swing;
++    requires javafx.baseEmpty;
++    requires javafx.controlsEmpty;
++    requires javafx.fxmlEmpty;
++    requires javafx.graphicsEmpty;
++    requires javafx.swingEmpty;
+     requires jdk.xml.dom;
+-    requires jfreechart;
+-    requires log4j;
++    requires jfreechart.debian;
+     requires org.apache.logging.log4j;
+     requires org.apache.logging.log4j.core;
+-    requires swing.layout;
++    requires swing.layout.debian;
+ }

debian/patches/series

 # fix_samtools_api
+fix_gradle.patch