New upstream version 2.6.3+dfsg (49a69b14) · Commits · Debian Med / igv

.gitignore

+1 −1

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

.travis.yml

+3 −3

Original line number	Diff line number	Diff line
		@@ -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

+12 −13

Original line number	Diff line number	Diff line
		# 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

+3 −2

Original line number	Diff line number	Diff line
		@@ -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

+138 −101

Original line number	Diff line number	Diff line
		@@ -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