.gitignore

@@ -2,7 +2,7 @@
 .idea/workspace.xml
 test/data/out/
 /build
-/build_java9
+/build_java11
 /bin
 igv.log
 /.gradle

.travis.yml

@@ -6,10 +6,10 @@ cache:
   directories:
     - $HOME/.gradle/caches/
     - $HOME/.gradle/wrapper/
-jdk: openjdk10
+jdk: openjdk11
 install:
-- ./gradlew -b build_java9.gradle assemble
+- ./gradlew -b build_java11.gradle assemble
 script:
-- ./gradlew -b build_java9.gradle check
+- ./gradlew -b build_java11.gradle check
 - jdk_switcher use openjdk8
 - ./gradlew compileJava
\ No newline at end of file

README.md

 # igv
 [![Build Status](https://travis-ci.org/igvteam/igv.svg?branch=master)](https://travis-ci.org/igvteam/igv)
 
-Integrative Genomics Viewer - dekstop genome visualization tool for Mac, Windows, and Linux.
+Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows, and Linux.
 
 ### Building
 
@@ -14,8 +14,8 @@ You may need to execute 'gradle wrapper' to set up the gradle wrapper.  This sho
 first time only, or if you clean up the local .gradle directory.  Only do this if the './gradlew' calls
 fail.
 
-There are two different build options, one for Java 8 and another for Java 9 and up.  The default is 
-to build for Java 8.  Java 8 builds are *NOT* compatible with Java 9 and vice versa.  
+There are two different build options, one for Java 8 and another for Java 11.  The default is 
+to build for Java 8.  Java 8 builds are *NOT* compatible with Java 11 and vice versa.  
 
 There are other options but these cover the most common uses:
 
@@ -35,7 +35,7 @@ NOTE: If on a Windows platform use ```./gradlew.bat'``` in the instructions belo
     * All four JARs must be in the same location in order to run IGV.  It can be run directly from
     'build/IGV-dist' 
     
-  *  Launch with 'igv.sh' on UNIX, 'igv.command' on Mac, and 'igv.bat' on Windows.  These scripts can
+  *  Launch with 'igv.sh' on UNIX, 'igv.command' on Mac, and 'igv.bat' (or 'igv_32.bat' for 32-bit Java) on Windows.  These scripts can
     be edited to adjust JVM flags like maximum memory, etc.  
     
   *  All other runtime dependencies are bundled into igv.jar.  There is also an igv-minimal.jar in
@@ -54,17 +54,16 @@ NOTE: If on a Windows platform use ```./gradlew.bat'``` in the instructions belo
 
 Note that Gradle creates a number of other subdirectories in 'build'.  These can be safely ignored.
 
-#### Java 9
+#### Java 11
 
-The instructions for Java 9 are nearly identical other than the need to specify the Java 9 build file
-and that the results will be found in 'build_java9' rather than 'build'.  More specifically:
+The instructions for Java 11 are nearly identical other than the need to specify the Java 11 build file
+and that the results will be found in 'build_java11' rather than 'build'.  More specifically:
 
-* Use './gradlew -b build_java9.gradle createDist' to build a distribution directory with helper scripts
+* Use ```./gradlew -b build_java11.gradle createDist``` to build a distribution directory with helper scripts
   for launching.  The structure is slightly different but the concept is the same.
   
-* Use './gradlew -b build_java9.gradle createToolsDist' for the igvtools distribution.
+* Use ```./gradlew -b build_java11.gradle test``` to run the test suite.
 
-* Use './gradlew -b build_java9.gradle test' to run the test suite.
-
-The full JAR build option is *NOT* available for Java 9+ because of modularity requirements.
+The full JAR build option is *NOT* available for Java 11 because of modularity requirements.  Also, there is no 
+separate igvtools distribution on Java 11; at present, this is folded into the normal IGV client distribution.
 

build.gradle

@@ -61,7 +61,7 @@ dependencies {
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '4.4.1'
+    gradleVersion = '4.10.1'
 }
 
 sourceCompatibility = 1.8
@@ -185,6 +185,7 @@ tasks.withType(Test) {
 task createDist(type: Copy, dependsOn: fullJar)  {
     from ("scripts") {
         include 'igv.bat'
+        include 'igv_32.bat'
         include 'igv.command'
         include 'igv.sh'
         include 'readme.txt'
@@ -306,7 +307,7 @@ task createToolsDistZip(type: Zip, dependsOn: createToolsDist) {
     baseName = "IGVTools"
 
     from "${buildDir}/IGVTools-dist"
-    into createToolsDistZip.baseName
+    into createToolsDistZip.baseName + "_${version}"
 
     doLast {
         project.exec { commandLine('chmod', '775', createToolsDistZip.archivePath ) }

build_java9.gradle → build_java11.gradle

@@ -26,14 +26,14 @@ import org.apache.tools.ant.filters.ReplaceTokens
 ext.moduleName = 'org.igv'
 ext.mainClassName = 'org.broad.igv.ui.Main'
 
-// Put the Java 9 build into a special dir to avoid accidental collisions.
-// Despite this, it is recommended that Java 8 vs. 9 builds be run in different locations.
-buildDir = 'build_java9' 
+// Put the Java 11 build into a special dir to avoid accidental collisions.
+// Despite this, it is recommended that Java 8 vs. 11 builds be run in different locations.
+buildDir = 'build_java11'
 
 sourceSets {
     main {
         java {
-            srcDirs = ['src/main/java', 'src/main/java9']
+            srcDirs = ['src/main/java', 'src/main/java11']
         }
         resources {
             srcDirs = ['src/main/resources', 'src/main/resources-jlfgr-1_0']
@@ -41,19 +41,23 @@ sourceSets {
         }
     }
 }
+configurations {
+    jarsForClasspath
+}
 
 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 fileTree(dir: 'lib', include: '*.jar')
     testCompile fileTree(dir: 'test/lib', include: '*.jar')
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '4.4.1'
+    gradleVersion = '4.10.2'
 }
 
-sourceCompatibility = 1.9
-targetCompatibility = 1.9
+// Gradle bug prevents us from generating Java 11 bytecode: https://github.com/gradle/gradle/issues/5120
+// Workaround is to target Java 10 for now.
+sourceCompatibility = 10
+targetCompatibility = 10
 
 processResources {
     // Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
@@ -78,20 +82,6 @@ jar {
     }
 }
 
-task tooljar(type: Jar, dependsOn: jar) {
-    // This jar is the same as the client jar above, just a different jar name and manifest
-    archiveName = 'igvtools.jar'
-    from(sourceSets.main.output) { }
-    
-    manifest {
-        attributes(
-            "Implementation-Title": "IGVTools",
-            "Built-By": System.getProperty('user.name'),
-            "Main-Class": "org.broad.igv.tools.IgvTools",
-        )
-    }
-}
-
 compileJava {
     inputs.property("moduleName", moduleName)
     doFirst {
@@ -129,14 +119,14 @@ test {
     inputs.property("moduleName", moduleName)
     doFirst {
         jvmArgs = [
+            '-Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize',
             '--module-path',  classpath.asPath, 
             '--add-modules', 'junit', 
             '--add-modules', 'fest.swing', 
-            '--add-modules', 'java.xml.bind', 
             '--add-modules', 'ALL-MODULE-PATH',
             '--add-reads', "$moduleName=junit", 
             '--add-reads', "$moduleName=fest.swing",
-            '@scripts/java9/test_suite.args',
+            '@scripts/java11/test_suite.args',
             '--patch-module', "$moduleName=" + files(sourceSets.test.java.outputDir, sourceSets.main.output.resourcesDir).asPath, 
         ]
         classpath = files()
@@ -144,130 +134,177 @@ test {
 }
 
 task createDist(type: Copy, dependsOn: jar)  {
-    from ('scripts/java9') {
-        include 'igv.bat'
+    from ("web/IGV_64.png")
+    from ('scripts/java11') {
+        include '*.bat'
+        include '*.sh'
         include 'igv.command'
-        include 'igv.sh'
-        include 'igv_hidpi.*'
         include 'igv.args'
         include 'readme.txt'
+        include 'igvtools*'
     }
-    
     with copySpec {
-        from ("lib") {
-            include '*.jar'
-            exclude 'jide-oss-3.5.5.jar'
-        }
-        from ("lib_java9") {
-            include '*.jar'
-        }
-        from ("${buildDir}/libs") {
-            include 'igv.jar'
-        }
+        from ("${buildDir}/libs")
+        from ("lib") { include '*.jar' }
         into "lib"
     }
+    with copySpec { from ("genomes/sizes") { } into "lib/genomes" }
 
     into "${buildDir}/IGV-dist"
 }
 
 task createDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_${version}_java10.zip"
+    archiveName = "IGV_${version}.zip"
     destinationDir = file("${buildDir}/distZip")
     baseName = "IGV"
-    from "${buildDir}/IGV-dist" exclude "*.bat"
-    into createDistZip.baseName + "_${version}_java10"
+    from ("${buildDir}/IGV-dist")
+    into createDistZip.baseName + "_${version}"
 
     doLast {
         project.exec { commandLine('chmod', '775', createDistZip.archivePath ) }
     }
 }
 
-task createMacDist(type: Copy, dependsOn: createDist) {
+task createLinuxDistZip(type: Zip, dependsOn: createDist) {
+    baseName = "IGV_Linux"
+    archiveName = createLinuxDistZip.baseName + "_${version}.zip"
+    destinationDir = file("${buildDir}/distZip")
+    if (!jdkBundleLinux.equals("")) {
+        with copySpec { from jdkBundleLinux into "jdk-11" }
+    }
+    from ("${buildDir}/IGV-dist") {
+        exclude "*.bat"
+        exclude "*.command"
+        exclude 'igvtools*'
+        exclude 'lib/genomes'
+    }
+    into createLinuxDistZip.baseName + "_${version}"
+
+    doLast {
+        project.exec { commandLine('chmod', '775', createLinuxDistZip.archivePath) }
+    }
+}
+
+task createMacDistZip(type: Zip, dependsOn: createDist) {
+    baseName = "IGV_Mac"
+    archiveName = createMacDistZip.baseName + "_${version}.zip"
+    destinationDir = file("${buildDir}/distZip")
+    if (!jdkBundleMac.equals("")) {
+        with copySpec { from jdkBundleMac into "jdk-11" }
+    }
+    from ("${buildDir}/IGV-dist") {
+        exclude "*.bat"
+        exclude "*_hidpi*"
+        exclude "igvtools*"
+        exclude 'lib/genomes'
+    }
+    into createMacDistZip.baseName + "_${version}"
+
+    doLast {
+        project.exec { commandLine('chmod', '775', createMacDistZip.archivePath ) }
+    }
+}
+
+task createMacAppDist(type: Copy, dependsOn: createDist) {
+    if (!jdkBundleMac.equals("")) {
+        with copySpec { from jdkBundleMac into "IGV_${version}.app/Contents/jdk-11" }
+    }
     with copySpec {
-        from ("scripts/mac.app") exclude "Contents/Info.plist.template"
-        into "IGV_${version}_java10.app"
+        from ("scripts/mac.app") {
+            exclude "Contents/Info.plist.template"
+            exclude "Contents/MacOS/JavaAppLauncher"
+        }
+        into "IGV_${version}.app"
     }
     with copySpec {
-        from ("scripts/java9/Info.plist.template")
+        from ("scripts/java11/Info.plist.template")
         filter (ReplaceTokens, tokens: [ VERSION: version ])
         rename "Info.plist.template", "Info.plist"
-        into "IGV_${version}_java10.app/Contents"
+        into "IGV_${version}.app/Contents"
+    }
+    with copySpec {
+        from ("scripts/java11/IGV_mac.app.command")
+        rename "IGV_mac.app.command", "IGV"
+        into "IGV_${version}.app/Contents/MacOS"
+    }
+    with copySpec {
+        from ("web/IGV_64.png")
+        into "IGV_${version}.app/Contents/Resources"
+    }
+    with copySpec {
+        from ("${buildDir}/IGV-dist/") include 'igv.args'
+        into "IGV_${version}.app/Contents/Java/"
     }
     with copySpec {
         from ("${buildDir}/IGV-dist/lib") include '*.jar'
-        into "IGV_${version}_java10.app/Contents/Java"
+        into "IGV_${version}.app/Contents/Java/lib"
     }
-
-    into "${buildDir}/IGV-Mac-dist"
+    into "${buildDir}/IGV-MacApp-dist"
 
     doLast {
-        project.exec { commandLine('chmod', '775', "${buildDir}/IGV-Mac-dist/IGV_${version}_java10.app" ) }
+        project.exec { commandLine('chmod', '775', "${buildDir}/IGV-MacApp-dist/IGV_${version}.app" ) }
     }
 }
 
-task createMacDistZip(type: Zip, dependsOn: createMacDist) {
-    archiveName = "IGV_${version}_java10.app.zip"
+task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) {
+    archiveName = "IGV_${version}.app.zip"
     destinationDir = file("${buildDir}/distZip")
-    from "${buildDir}/IGV-Mac-dist"
+    from "${buildDir}/IGV-MacApp-dist"
     
     doLast {
-        project.exec { commandLine('chmod', '775', createMacDistZip.archivePath ) }
+        project.exec { commandLine('chmod', '775', createMacAppDistZip.archivePath ) }
     }
 }
 
-task createWinDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Win_${version}_java10.zip"
-    destinationDir = file("${buildDir}/distZip")
-    baseName = "IGV_Win"
+task createWinDist(type: Copy, dependsOn: createDist) {
+    if (!jdkBundleWindows.equals("")) {
+        with copySpec { from jdkBundleWindows into "IGV_${version}/jdk-11" }
+    }
+    with copySpec {
         from("${buildDir}/IGV-dist") {
             exclude "*.sh"
-        exclude "igv.command"
-    }
-    into createWinDistZip.baseName + "_${version}_java10"
-
-    doLast {
-        project.exec { commandLine('chmod', '775', createWinDistZip.archivePath ) }
-    }
+            exclude "*.command"
+            exclude "igvtools*"
+            exclude "igvtools_gui"
+            exclude "igvtools_gui_hidpi"
+            exclude 'lib/genomes'
         }
-
-task createToolsDist(type: Copy, dependsOn: tooljar)  {
-    from ("scripts/java9") {
-        include 'igvtools*'
-        include 'igvtools*.bat'
-        include 'igvtools*.command'
-        include 'igv.args'
+        from ("resources") { include "IGV_64.ico" }
+        into "IGV_${version}"
     }
-    
     with copySpec {
-        from ("${buildDir}/libs") {
-            include 'igvtools.jar'
+        // Create a build-specific NSIS installer script.
+        from ("scripts/nsis/installer.nsi")
+        filter (ReplaceTokens, tokens: [ VERSION: version ])
     }
-        from ("lib") {
-            include '*.jar'
-            exclude 'jide-oss-3.5.5.jar'
+    from ("scripts/nsis") { include "license_win.txt" }
+    into "${buildDir}/IGV-WinExe-dist"
 }
-        from ("lib_java9") {
-            include '*.jar'
+
+task createWinExeDist(type: Exec, dependsOn: createWinDist) {
+    commandLine(makensisCommand, "-O${buildDir}/tmp/nsis-build.log",
+                "${buildDir}/IGV-WinExe-dist/installer.nsi")
+    doLast {
+        if (makensisCommand.equals("")) {
+            throw new GradleException("Required property not set: makensisCommand");
         }
-        into "lib"
     }
-
-    with copySpec { from ("genomes/sizes") { } into "lib/genomes" }
-
-    into "${buildDir}/IGVTools-dist"
 }
         
-task createToolsDistZip(type: Zip, dependsOn: createToolsDist) {
-    archiveName = "igvtools_${version}_java10.zip"
-    destinationDir = file("${buildDir}/distZip")
-    baseName = "IGVTools_java10"
-    
-    from "${buildDir}/IGVTools-dist"
-    into createToolsDistZip.baseName
-
+task signWinExeDist(type: Exec, dependsOn: createWinExeDist) {
+    standardInput = new ByteArrayInputStream( keyPassword.getBytes() );
+    commandLine(signcodeCommand, "-spc", spcFile, "-v", pvkFile, "-a", "sha1", 
+                "-\$", "commercial", "-n", "IGV ${version}", "-i", "http://www.igv.org/",
+                "-t", tsaurl, "-tr", "10", "${buildDir}/IGV-WinExe-dist/IGV_Win_${version}-installer.exe")
     doLast {
-        project.exec { commandLine('chmod', '775', createToolsDistZip.archivePath ) }
+        if (signcodeCommand.equals("")) {
+            throw new GradleException("Required property not set: signcodeCommand");
+        }
     }
 }
 
-build.dependsOn createDistZip,createMacDistZip,createWinDistZip,createToolsDistZip
+build.dependsOn createDistZip,createLinuxDistZip,createMacDistZip,createMacAppDistZip
+
+if (!makensisCommand.equals("") && !signcodeCommand.equals("")) {
+    build.dependsOn signWinExeDist
+}
\ No newline at end of file

debian/changelog

+igv (2.6.3+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Sep 2019 14:58:15 +0200
+
 igv (2.4.17+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-12

debian/control

@@ -6,7 +6,7 @@ Section: non-free/science
 XS-Autobuild: yes
 Priority: optional
 Build-Depends: default-jdk,
-               debhelper (>= 12~),
+               debhelper-compat (= 12),
                gradle-debian-helper,
                junit4,
                libbatik-java,
@@ -32,7 +32,7 @@ Build-Depends: default-jdk,
                libswing-layout-java,
                libxml-commons-external-java,
                libguava-java,
-               libbcprov-java (>= 1.47),
+               libbcprov-java,
                libjgrapht0.8-java,
                libgoogle-gson-java,
                javahelper,
@@ -41,7 +41,7 @@ Build-Depends: default-jdk,
                libfest-util-java,
                libfest-reflect-java,
                ant
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/igv
 Vcs-Git: https://salsa.debian.org/med-team/igv.git
 Homepage: http://www.broadinstitute.org/igv/

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: 2018-10-17
-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.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 +54,29 @@
- 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')
-+    compile files ("/usr/share/maven-repo/org/openjfx/javafx-graphics/debian/javafx-graphics-debian-linux.jar")
-+    compile files ("/usr/share/maven-repo/org/openjfx/javafx-controls/debian/javafx-controls-debian-linux.jar")
-+    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 "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-1.2-api:debian"
-+    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 +84,8 @@
-     gradleVersion = '4.4.1'
- }
- 
--sourceCompatibility = 1.9
--targetCompatibility = 1.9
-+//sourceCompatibility = 1.11
-+//targetCompatibility = 1.11
- 
- processResources {
-     // Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
-@@ -93,12 +125,9 @@
- }
- 
- compileJava {
--    inputs.property("moduleName", moduleName)
-+    //inputs.property("moduleName", moduleName)
-     doFirst {
--        options.compilerArgs = [
--            '--module-path', classpath.asPath,
--        ]
--        classpath = files()
-+    //    classpath = files()
-     }
- }
- 
---- a/src/main/java9/module-info.java
-+++ b/src/main/java9/module-info.java
-@@ -5,11 +5,11 @@
-     
-     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;
-@@ -22,5 +22,5 @@
-     requires log4j;
-     requires org.apache.logging.log4j;
-     requires org.apache.logging.log4j.core;
--    requires swing.layout;
-+    requires swing.layout.debian;
- }
---- 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 @@
-         return actualSkip;
-     }
- 
--    @Override
--    public synchronized void reset() throws IOException {
--
--        if (markpos < 0) {
--            throw new IOException("Resetting to invalid mark");
--        }
--        position = markpos;
--
--    }
--
-     public void seek(final long position) throws IOException {
-         this.position = position;
-     }
-@@ -215,4 +205,4 @@
-             bufferSize = tmpBufferSize;
-         }
-     }
--}
-\ No newline at end of file
-+}

debian/patches/series

 # fix_samtools_api
-fix_gradle.patch

debian/rules

@@ -19,7 +19,7 @@ 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 -a build_java11.gradle build.gradle
+	# mv src/main/java9/module-info.java src/main/java9/module-info.java.skip
 	cp debian/log4j.xml src/main/resources/
 	cp /usr/share/java/jaxb-api.jar $(CURDIR)/lib/

genomes/db/1kg_ref/1kg_ref_dataServerRegistry.txt

+http://www.broadinstitute.org/igvdata/annotations/hg18/hg18_annotations.xml
+http://www.broadinstitute.org/igvdata/hg18/Metabric/metabric.xml
+http://igv.broadinstitute.org/data/hg18/tcga/tcga_external.xml
+http://www.broadinstitute.org/igvdata/Tumorscape/Tumorscape.xml
+http://www.broadinstitute.org/igvdata/encode/hg18/hg18_encode_color.xml
+http://www.broadinstitute.org/igvdata/epigenetics/epigenetics_hg18_public.xml
+http://www.broadinstitute.org/igvdata/epigenetics/WilmsTumor/wilms_tumor.xml
+http://www.broadinstitute.org/igvdata/29mammals/29mammals.xml
+http://www.broadinstitute.org/igvdata/BodyMap/BodyMap.xml
+http://www.broadinstitute.org/igvdata/tutorials/tutorials.xml
+

genomes/db/1kg_v37/1kg_v37_dataServerRegistry.txt

+https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_annotations.xml
+http://gdac.broadinstitute.org/tap/igv/load/tcga_hg19.xml
+http://www.broadinstitute.org/igvdata/encode/hg19/hg19_encode.xml
+http://www.broadinstitute.org/igvdata/1KG/b37/1KG.s3.xml
+http://www.broadinstitute.org/igvdata/tutorials/tutorials.hg19.xml
\ No newline at end of file

genomes/db/D.discoideum/D.discoideum_dataServerRegistry.txt

+http://www.broadinstitute.org/igvdata/annotations/D.discoideum/D.discoideum_annotations.xml

genomes/db/GSM552910/GSM552910_dataServerRegistry.txt

+http://igv.broadinstitute.org/data/GSM552910/GSM552910.xml
\ No newline at end of file

genomes/db/S_pombe_709/S_pombe_709_dataServerRegistry.txt

+http://www.broadinstitute.org/igvdata/annotations/pombe/spombe_annotations.xml
+

genomes/db/WS241/ws241_dataServerRegistry.txt

+http://www.broadinstitute.org/igvdata/ws241_annotations.xml
\ No newline at end of file

genomes/db/b37/b37_dataServerRegistry.txt

+https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_annotations.xml
+http://gdac.broadinstitute.org/tap/igv/load/tcga_hg19.xml
+http://www.broadinstitute.org/igvdata/encode/hg19/hg19_encode.xml
+http://www.broadinstitute.org/igvdata/1KG/b37/1KG.s3.xml
+http://www.broadinstitute.org/igvdata/tutorials/tutorials.hg19.xml
\ No newline at end of file

genomes/db/canFam2/canFam2_dataServerRegistry.txt

+http://igvdata.broadinstitute.org/data/canFam2/canFam2_annotations.xml