zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix an issue with the classpath for external builds in build.xml 

Use "path" instead of "pathconvert" to construct the external.gatk.classpath.
This allows the path to evolve as the build progresses, instead of being
fixed early on to a value that (in some cases) could be incorrect.
This commit is contained in:
David Roazen 2012-08-15 15:56:54 -04:00
parent db92671b7f
commit 9b84fa20bf
1 changed files with 9 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

23
build.xml
View File

@ -70,13 +70,18 @@
<property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
<property name="R.script.staging.dir" value="${build.dir}/R/stage" />
<!-- Properties used for external builds -->
<property name="external.build.dir" value="${java.classes}" />
<property name="external.dist.dir" value="${dist.dir}" />
<!-- Packaging system properties -->
<property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" />
<property name="staging.dir" value="staging" />
<property name="default.executable" value="none" />
<!-- Javadoc/Scaladoc directories -->
<!-- GATKDocs/Javadoc/Scaladoc directories -->
<property name="gatkdocs.dir" value="gatkdocs" />
<property name="javadoc.dir" value="javadoc" />
<property name="scaladoc.dir" value="scaladoc" />
@ -96,8 +101,6 @@
<property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
<property name="contract.dump.dir" value="dump" />
<property name="gatkdocs.dir" value="gatkdocs" />
<!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
<property name="halt" value="yes" />
@ -208,19 +211,11 @@
<include name="**/*.java" />
</fileset>
<pathconvert property="external.build.dir">
<path path="${java.classes}"/>
</pathconvert>
<pathconvert property="external.dist.dir">
<path path="${dist.dir}" />
</pathconvert>
<!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
<pathconvert property="external.gatk.classpath">
<path id="external.gatk.classpath">
<path path="${java.classes}"/>
<path refid="external.dependencies" />
</pathconvert>
</path>
<!-- the path for resources that need to go into the GATK jar;
any additional resources should go into this set. -->
@ -432,7 +427,7 @@
<subant target="compile" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" />
<property name="dist.dir" value="${external.dist.dir}" />
<property name="gatk.classpath" value="${external.gatk.classpath}" />
<property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</target>