59 lines
2.8 KiB
XML
59 lines
2.8 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
|
|
<!--
|
|
~ Copyright (c) 2011, The Broad Institute
|
|
~
|
|
~ Permission is hereby granted, free of charge, to any person
|
|
~ obtaining a copy of this software and associated documentation
|
|
~ files (the "Software"), to deal in the Software without
|
|
~ restriction, including without limitation the rights to use,
|
|
~ copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
~ copies of the Software, and to permit persons to whom the
|
|
~ Software is furnished to do so, subject to the following
|
|
~ conditions:
|
|
~
|
|
~ The above copyright notice and this permission notice shall be
|
|
~ included in all copies or substantial portions of the Software.
|
|
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
|
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
|
~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
|
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
|
~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
|
~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
~ OTHER DEALINGS IN THE SOFTWARE.
|
|
-->
|
|
|
|
<package name="GATKEngine">
|
|
<executable name="GATKEngine">
|
|
<dependencies>
|
|
<!-- Package everything in org.broadinstitute.sting -->
|
|
<package name="org.broadinstitute.sting.**" />
|
|
<!-- Tribble codecs -->
|
|
<package name="org.broad.tribble.**" />
|
|
<!-- Workaround - depend on the logger impl required by JEXL -->
|
|
<package name="org.apache.commons.logging.impl" />
|
|
<!-- R packages -->
|
|
<dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
|
|
<!-- All R scripts in org.broadinstitute.sting -->
|
|
<dir name="org/broadinstitute/sting" includes="**/*.R" />
|
|
<!-- The GATK public key -->
|
|
<file path="GATK_public.key" />
|
|
</dependencies>
|
|
</executable>
|
|
<resources>
|
|
<!-- Sample reads and reference files -->
|
|
<file name="public/testdata/exampleBAM.bam" />
|
|
<file name="public/testdata/exampleBAM.bam.bai" />
|
|
<file name="public/testdata/exampleFASTA.fasta" />
|
|
<file name="public/testdata/exampleFASTA.fasta.fai" />
|
|
<file name="public/testdata/exampleFASTA.dict" />
|
|
<!-- GATK sample code and build scripts -->
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java" />
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java" />
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java" />
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java" />
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java" />
|
|
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java" />
|
|
</resources>
|
|
</package>
|