79 lines
3.4 KiB
XML
79 lines
3.4 KiB
XML
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<?xml version="1.0" encoding="UTF-8"?>
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<!--
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~ Copyright (c) 2012, The Broad Institute
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~
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<package name="QueueEngine">
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<executable name="QueueEngine">
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<dependencies>
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<!-- Queue -->
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<package name="org.broadinstitute.sting.queue.**" />
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<!-- Pipeline + Utils -->
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<package name="org.broadinstitute.sting.pipeline.**" />
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<package name="org.broadinstitute.sting.utils.**" />
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<!-- Scala -->
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<package name="scala.**" />
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<!-- Picard -->
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<package name="net.sf.picard.**" />
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<package name="edu.mit.broad.picard.**" />
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<!-- JavaMail -->
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<package name="javax.activation.**" />
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<package name="javax.mail.**" />
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<package name="com.sun.activation.**" />
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<package name="com.sun.mail.**" />
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<file path="META-INF/javamail.charset.map" />
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<file path="META-INF/javamail.default.address.map" />
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<file path="META-INF/javamail.default.providers" />
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<file path="META-INF/mailcap" />
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<file path="META-INF/mailcap.default" />
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<file path="META-INF/mimetypes.default" />
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<!-- JNA, including embedded native libraries -->
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<dir name="com/sun/jna" />
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<!-- Contracts for Java -->
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<package name="com.google.java.contract.**" />
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<!-- snpEff -->
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<package name="ca.mcgill.mcb.pcingola.**" />
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<file path="snpEff_genes.ftl" />
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<file path="snpEff_summary.ftl" />
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<!-- R scripts -->
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<dir name="org/broadinstitute/sting/queue" includes="**/*.R" />
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</dependencies>
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</executable>
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<resources>
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<!-- Sample QScripts -->
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<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala" />
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<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala" />
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<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala" />
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<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala" />
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<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala" />
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</resources>
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</package>
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