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More cleanup. Make sure resources are unioned among all the specified modules. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2653 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-21 19:38:46 +00:00
parent 3e54e131e0
commit 4fc926232c
4 changed files with 20 additions and 21 deletions
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5
packages/AnalyzeCovariates.xml
View File

@ -13,4 +13,9 @@
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" /> <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
</dependencies> </dependencies>
</executable> </executable>
<resources>
<!-- Supplemental scripts for graph generation, etc. -->
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
</resources>
</package> </package>

30
packages/CreatePackager.xsl
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@ -40,21 +40,10 @@
<xsl:apply-templates select="document(@file)/package/executable" /> <xsl:apply-templates select="document(@file)/package/executable" />
</xsl:for-each> </xsl:for-each>
<!-- Include various script files --> <!-- Include various resource files explicitly specified in this file and in all other modules -->
<xsl:for-each select="scripts/file"> <xsl:apply-templates select="resources" />
<xsl:call-template name="symlink"> <xsl:for-each select="//modules/module">
<xsl:with-param name="file.name" select="@name" /> <xsl:apply-templates select="document(@file)/package/resources" />
<xsl:with-param name="target.dir" select="$package.dir" />
</xsl:call-template>
</xsl:for-each>
<!-- Include various resource files -->
<xsl:for-each select="resources/file">
<mkdir dir="{$resources.dir}"/>
<xsl:call-template name="symlink">
<xsl:with-param name="file.name" select="@name" />
<xsl:with-param name="target.dir" select="$resources.dir" />
</xsl:call-template>
</xsl:for-each> </xsl:for-each>
<!-- Bundle the package into a single zip file --> <!-- Bundle the package into a single zip file -->
@ -115,6 +104,17 @@
</jar> </jar>
</xsl:template> </xsl:template>
<!-- Transform a resource file into a symlink operation -->
<xsl:template match="resources">
<xsl:for-each select="file">
<mkdir dir="{$resources.dir}"/>
<xsl:call-template name="symlink">
<xsl:with-param name="file.name" select="@name" />
<xsl:with-param name="target.dir" select="$resources.dir" />
</xsl:call-template>
</xsl:for-each>
</xsl:template>
<!-- Transform a dependency list into a fileset for embedding in a jar --> <!-- Transform a dependency list into a fileset for embedding in a jar -->
<xsl:template match="dependencies"> <xsl:template match="dependencies">
<classfileset dir="{$staging.dir}"> <classfileset dir="{$staging.dir}">

3
packages/GATK-Picard.xml
View File

@ -47,8 +47,5 @@
<file name="testdata/exampleFASTA.fasta" /> <file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" /> <file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" /> <file name="testdata/exampleFASTA.dict" />
<!-- Supplemental scripts for graph generation, etc. -->
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
</resources> </resources>
</package> </package>

3
packages/GenomeAnalysisTK.xml
View File

@ -43,8 +43,5 @@
<file name="testdata/exampleFASTA.fasta" /> <file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" /> <file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" /> <file name="testdata/exampleFASTA.dict" />
<!-- Supplemental scripts for graph generation, etc. -->
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
</resources> </resources>
</package> </package>