diff --git a/build.gradle b/build.gradle index 1508dffb4..ab85c1039 100644 --- a/build.gradle +++ b/build.gradle @@ -104,6 +104,8 @@ configurations { exclude group: 'xalan', module: 'serializer' exclude group: 'xalan', module: 'xalan' + exclude group: 'org.xerial.snappy', module: 'snappy-java' + // Amazon deps exclusions //exclude group: 'software.amazon', module: 'flow' //exclude group: 'software.amazon.awssdk', module: 'annotations' @@ -122,7 +124,7 @@ dependencies { [group: 'org.apache.commons', name: 'commons-compress', version: '1.26.0'], [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'], [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'], - [group: 'com.github.samtools', name: 'htsjdk', version: '4.1.1'], + [group: 'com.github.samtools', name: 'htsjdk', version: '4.1.2'], [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'], [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'], [group: 'com.google.guava', name: 'guava', version: '32.1.3-jre'], @@ -359,7 +361,8 @@ tasks.register('createMacAppWithJavaDistZip', Zip) { } } -task createWinDist(type: Copy, dependsOn: createDist) { +tasks.register('createWinDist', Copy) { + dependsOn createDist with copySpec { from("${buildDir}/IGV-dist") { exclude "*.sh" @@ -440,7 +443,8 @@ tasks.register('signWinExeDist', Exec) { } } -task signWinExeWithJavaDist(type: Exec, dependsOn: createWinWithJavaExeDist) { +tasks.register('signWinExeWithJavaDist', Exec) { + dependsOn createWinWithJavaExeDist standardInput = new ByteArrayInputStream(keyPassword.getBytes()); commandLine(signcodeCommand, "-spc", spcFile, "-v", pvkFile, "-a", "sha512", "-\$", "commercial", "-n", "IGV ${version}", "-i", "http://www.igv.org/", @@ -452,7 +456,8 @@ task signWinExeWithJavaDist(type: Exec, dependsOn: createWinWithJavaExeDist) { } } -task fullJar(type: Jar, dependsOn: jar) { +tasks.register('fullJar', Jar) { + dependsOn jar // Based on https://discuss.gradle.org/t/removing-dependencies-from-a-jar-file-during-jar-task/5521/3 from { ((configurations.compile - configurations.default) + "${buildDir}/libs/igv.jar").collect {