[med-svn] [picard-tools] 04/04: Take over patches from previous version
Andreas Tille
tille at debian.org
Sun Mar 13 11:25:12 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository picard-tools.
commit 9679a96cc91d8409d258bc452a4f5589f0e2d4db
Author: Andreas Tille <tille at debian.org>
Date: Sun Mar 13 12:16:34 2016 +0100
Take over patches from previous version
---
debian/patches/10-build.xml | 84 ++++++++++++++++-----------------------------
1 file changed, 29 insertions(+), 55 deletions(-)
diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml
index a7cc494..e84a9b4 100644
--- a/debian/patches/10-build.xml
+++ b/debian/patches/10-build.xml
@@ -4,17 +4,15 @@ Description: Modifies the upstream build system.
and get htsjdk version from system jar.
Origin: vendor
Forwarded: no
-Index: picard-tools/build.xml
-===================================================================
---- picard-tools.orig/build.xml
-+++ picard-tools/build.xml
+--- a/build.xml
++++ b/build.xml
@@ -42,17 +42,16 @@
<property name="htsjdk_git_url" value="git at github.com:samtools/htsjdk.git"/>
<!-- TODO: get this from the build.xml in htsjdk -->
<property name="htsjdk-classes" value="htsjdk/classes"/>
+ <property name="htsjdk-jar" value="/usr/share/java/htsjdk.jar"/>
- <property name="javac.target" value="1.6"/>
+ <property name="javac.target" value="1.8"/>
<property name="javac.debug" value="true"/>
<!-- Get GIT hash, if available, otherwise leave it blank. -->
@@ -28,10 +26,10 @@ Index: picard-tools/build.xml
+ packaging repo), but use the "dfsg" string as sources are
+ repacked -->
+ <property name="repository.revision" value="dfsg"/>
- <property name="picard-version" value="1.138"/>
+ <property name="picard-version" value="2.1.1"/>
<property name="command-line-html-dir" value="${dist}/html"/>
<property name="testng.verbosity" value="2"/>
-@@ -77,23 +76,17 @@
+@@ -83,23 +82,17 @@
<!-- INIT -->
<target name="init">
<path id="classpath">
@@ -45,8 +43,8 @@ Index: picard-tools/build.xml
- <include name="**/*.jar"/>
- </fileset>
- <fileset dir="${lib}">
-- <include name="**/*.jar"/>
-- </fileset>
+- <include name="**/*.jar"/>
+- </fileset>
+ <!-- for the HTSJDK library JAR -->
+ <pathelement path="/usr/share/java/htsjdk.jar"/>
+ <!-- other system required installed JARs -->
@@ -62,7 +60,7 @@ Index: picard-tools/build.xml
</path>
</target>
-@@ -107,23 +100,13 @@
+@@ -113,23 +106,13 @@
<delete dir="javadoc"/>
</target>
@@ -89,7 +87,7 @@ Index: picard-tools/build.xml
</target>
<target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge">
-@@ -165,13 +148,13 @@
+@@ -171,13 +154,13 @@
description="Compile files without cleaning">
</target>
@@ -105,46 +103,41 @@ Index: picard-tools/build.xml
<target name="compile-picard-tests" depends="init" description="Compile picard test files without cleaning">
<compile-tests includes="picard/**/*.*"/>
-@@ -199,6 +182,7 @@
+@@ -260,6 +243,8 @@
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
+ <pathelement path="/usr/share/java/jcommander.jar"/>
- </classpath>
- <classfileset dir="${classes.test}">
- <include name="**/Test*.class"/>
-@@ -234,6 +218,7 @@
- <pathelement path="${classes}"/>
- <pathelement path="${classes.test}"/>
- <pathelement path="${scripts}"/>
+ <pathelement path="/usr/share/java/jcommander.jar"/>
</classpath>
<classfileset dir="${classes.test}">
<include name="**/${name}.class"/>
-@@ -258,21 +243,17 @@
- </unzip>
+@@ -284,7 +269,7 @@
+ </unzip>
</target>
-
+
- <target name="picard-jar" depends="compile, process-external-jars"
+ <target name="picard-jar" depends="compile, process-external-jars, set-htsjdk-version"
- description="Builds the main executable picard.jar">
- <mkdir dir="${dist}"/>
- <mkdir dir="${dist.tmp}"/>
- <unjar dest="${dist.tmp}">
- <fileset dir="${lib}" />
-- <fileset dir="${htsjdk_lib_dir}">
-- <include name="*.jar"/>
-- </fileset>
- </unjar>
+ description="Builds the main executable picard.jar">
+ <mkdir dir="${dist}"/>
+ <mkdir dir="${dist.tmp}"/>
+@@ -292,15 +277,11 @@
+ <fileset dir="${lib}">
+ <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing -->
+ </fileset>
+- <fileset dir="${htsjdk_lib_dir}">
+- <include name="*.jar"/>
+- </fileset>
+ </unjar>
<jar destfile="${dist}/picard.jar" compress="no">
<fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/>
<fileset dir="${src.scripts}" includes="**/*.R"/>
- <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/>
<fileset dir="${dist.tmp}" includes="**/*"/>
- <fileset dir="${jar_opt}" includes="**/*"/>
+ <fileset dir="${jar_opt}" includes="**/*"/>
-@@ -319,43 +300,17 @@
+@@ -348,44 +329,17 @@
<fileset dir="${lib}">
<include name="**/*.jar"/>
</fileset>
@@ -175,6 +168,7 @@ Index: picard-tools/build.xml
- protected="true"
- use="true"
- version="true"
+- additionalparam="-Xdoclint:none -notimestamp"
- failonerror="true"
- excludepackagenames="picard*">
- <classpath>
@@ -194,7 +188,7 @@ Index: picard-tools/build.xml
<mkdir dir="${command-line-html-dir}"/>
<javadoc doclet="picard.util.MetricsDoclet"
docletpathref="metrics.classpath"
-@@ -366,13 +321,12 @@
+@@ -396,13 +350,12 @@
<fileset dir="${lib}">
<include name="**/*.jar"/>
</fileset>
@@ -211,27 +205,7 @@ Index: picard-tools/build.xml
</fileset>
<arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/>
</javadoc>
-@@ -477,6 +431,9 @@
- failonerror="true">
- <classpath>
- <pathelement location="${dist}/picard.jar"/>
-+ <pathelement path="/usr/share/java/htsjdk.jar"/>
-+ <pathelement path="/usr/share/java/guava.jar"/>
-+ <pathelement path="/usr/share/java/testng.jar"/>
- </classpath>
- </java>
- </sequential>
-@@ -498,6 +455,9 @@
- failonerror="true">
- <classpath>
- <pathelement location="${dist}/picard.jar"/>
-+ <pathelement path="/usr/share/java/htsjdk.jar"/>
-+ <pathelement path="/usr/share/java/guava.jar"/>
-+ <pathelement path="/usr/share/java/testng.jar"/>
- </classpath>
- <arg value="@{main-class}"/>
- </java>
-@@ -561,4 +521,25 @@
+@@ -617,4 +570,25 @@
</javac>
</sequential>
</macrodef>
--
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