Olivier Sallou pushed to branch master at Debian Med / igv
Commits:
aa58fc0f by Olivier Sallou at 2018-12-18T08:01:31Z
add ant dependency
- - - - -
eaa4f44b by Olivier Sallou at 2018-12-18T09:34:46Z
add ant to java depends and build
- - - - -
4 changed files:
- debian/bin/igv
- debian/changelog
- debian/control
- debian/patches/fix_gradle.patch
Changes:
=====================================
debian/bin/igv
=====================================
@@ -1,5 +1,5 @@
#!/bin/sh
set -eu
-exec java -cp
/usr/share/java/jaxb-api.jar:/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 "$@"
+exec java -cp
/usr/share/java/ant.jar:/usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar
org.broad.igv.ui.Main "$@"
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-igv (2.4.16+dfsg-1) UNRELEASED; urgency=medium
+igv (2.4.16+dfsg-1) unstable; urgency=medium
* New upstream version
* Drop Build-Depends: libmysql-java, Recommends: libmariadb-java
=====================================
debian/control
=====================================
@@ -39,7 +39,8 @@ Build-Depends: default-jdk,
libjide-oss-java,
libfest-assert-java,
libfest-util-java,
- libfest-reflect-java
+ libfest-reflect-java,
+ ant
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/igv
Vcs-Git: https://salsa.debian.org/med-team/igv.git
=====================================
debian/patches/fix_gradle.patch
=====================================
@@ -5,7 +5,7 @@ Description: gradle build file needs to add debian based
libraries
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 <[email protected]>
-Last-Updated: 2018-10-15
+Last-Updated: 2018-10-17
Forwarded: no
--- a/build_java9.gradle
+++ b/build_java9.gradle
@@ -21,7 +21,7 @@ Forwarded: no
import org.apache.tools.ant.filters.ReplaceTokens
ext.moduleName = 'org.igv'
-@@ -30,6 +33,12 @@ ext.mainClassName = 'org.broad.igv.ui.Ma
+@@ -30,6 +33,12 @@
// Despite this, it is recommended that Java 8 vs. 9 builds be run in
different locations.
buildDir = 'build_java9'
@@ -34,7 +34,7 @@ Forwarded: no
sourceSets {
main {
java {
-@@ -45,6 +54,28 @@ sourceSets {
+@@ -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')
@@ -60,10 +60,11 @@ Forwarded: no
+ 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 +83,8 @@ task wrapper(type: Wrapper) {
+@@ -52,8 +84,8 @@
gradleVersion = '4.4.1'
}
@@ -74,7 +75,7 @@ Forwarded: no
processResources {
// Set the current timestamp for release builds; pass in a blank property
to enable (i.e. -Ptimestamp="" at CLI)
-@@ -93,12 +124,9 @@ task tooljar(type: Jar, dependsOn: jar)
+@@ -93,12 +125,9 @@
}
compileJava {
@@ -91,7 +92,7 @@ Forwarded: no
--- a/src/main/java9/module-info.java
+++ b/src/main/java9/module-info.java
-@@ -5,11 +5,11 @@ module org.igv {
+@@ -5,11 +5,11 @@
requires AbsoluteLayout;
requires ant;
@@ -107,7 +108,7 @@ Forwarded: no
requires htsjdk;
requires java.datatransfer;
requires java.desktop;
-@@ -22,5 +22,5 @@ module org.igv {
+@@ -22,5 +22,5 @@
requires log4j;
requires org.apache.logging.log4j;
requires org.apache.logging.log4j.core;
@@ -116,7 +117,7 @@ Forwarded: no
}
--- 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 @@ public class IGVSeekableBufferedStream e
+@@ -87,16 +87,6 @@
return actualSkip;
}
@@ -133,7 +134,7 @@ Forwarded: no
public void seek(final long position) throws IOException {
this.position = position;
}
-@@ -215,4 +205,4 @@ public class IGVSeekableBufferedStream e
+@@ -215,4 +205,4 @@
bufferSize = tmpBufferSize;
}
}
View it on GitLab:
https://salsa.debian.org/med-team/igv/compare/f5e67620bd6119e91dddf7a57917b69eb25e1192...eaa4f44b997ae1463e5c3a59a319578e2789c608
--
View it on GitLab:
https://salsa.debian.org/med-team/igv/compare/f5e67620bd6119e91dddf7a57917b69eb25e1192...eaa4f44b997ae1463e5c3a59a319578e2789c608
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