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gatk-3.8
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Convert external.build.dir and external.dist.dir back to paths 

The previous push fixed the external classpath issue but broke external
builds in a new way by changing the above from paths to properties. This
was a mistake, since external builds require absolute, not relative, paths

Thanks to akiezun for the bug report and patch
This commit is contained in:
David Roazen 2012-08-15 22:54:13 -04:00
parent 9d09230c26
commit fa7605c643
1 changed files with 13 additions and 9 deletions
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22
build.xml
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@ -70,10 +70,6 @@
<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="${dist.dir}/packages" />
@ -211,6 +207,14 @@
<include name="**/*.java" />
</fileset>
<path id="external.build.dir">
<path path="${java.classes}" />
</path>
<path id="external.dist.dir">
<path path="${dist.dir}" />
</path>
<!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
<path id="external.gatk.classpath">
<path path="${java.classes}"/>
@ -425,8 +429,8 @@
<target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
<subant target="compile" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" />
<property name="dist.dir" value="${external.dist.dir}" />
<property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" refid="external.dist.dir" />
<property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
@ -675,9 +679,9 @@
</jar>
<subant target="dist" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" />
<property name="dist.dir" value="${external.dist.dir}" />
<property name="gatk.classpath" value="${external.gatk.classpath}" />
<property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" refid="external.dist.dir" />
<property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</target>