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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2012-08-15 23:13:32 -04:00
parent 9035b554fb fa7605c643
commit 04be0c92bf
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.package.path" value="org/broadinstitute/sting/utils/R" />
<property name="R.script.staging.dir" value="${build.dir}/R/stage" /> <property name="R.script.staging.dir" value="${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 --> <!-- Packaging system properties -->
<property name="package.xml.dir" value="${public.dir}/packages" /> <property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" /> <property name="package.output.dir" value="${dist.dir}/packages" />
@ -211,6 +207,14 @@
<include name="**/*.java" /> <include name="**/*.java" />
</fileset> </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 --> <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
<path id="external.gatk.classpath"> <path id="external.gatk.classpath">
<path path="${java.classes}"/> <path path="${java.classes}"/>
@ -425,8 +429,8 @@
<target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external"> <target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
<subant target="compile" genericantfile="build.xml"> <subant target="compile" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" /> <property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" value="${external.dist.dir}" /> <property name="dist.dir" refid="external.dist.dir" />
<property name="gatk.classpath" refid="external.gatk.classpath" /> <property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" /> <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant> </subant>
@ -675,9 +679,9 @@
</jar> </jar>
<subant target="dist" genericantfile="build.xml"> <subant target="dist" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" /> <property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" value="${external.dist.dir}" /> <property name="dist.dir" refid="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" /> <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant> </subant>
</target> </target>