Moved build.xml, ivy.xml, ivysettings.xml, ivy properties, public/packages/*.xml into private/archive/ant
This commit is contained in:
Khalid Shakir
David Roazen
parent
83d07280ef
commit
eb52dc6a9b
117
ivy.xml
117
ivy.xml
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@ -1,117 +0,0 @@
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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
|
||||
~ 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
|
||||
~ 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
|
||||
~ 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,
|
||||
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
~ 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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<ivy-module version="1.0">
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<info organisation="org.broadinstitute" module="Sting"/>
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<configurations>
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<conf name="default" description="the core dependencies for the GATK"/>
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</configurations>
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<dependencies defaultconf="default">
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<dependency org="net.sf" name="sam" rev="latest.integration"/>
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<dependency org="net.sf" name="picard" rev="latest.integration"/>
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<dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
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<!-- Tribble -->
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<dependency org="org.broad" name="tribble" rev="latest.integration"/>
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<!-- Variant -->
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<dependency org="org.broadinstitute" name="variant" rev="latest.integration"/>
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<dependency org="log4j" name="log4j" rev="1.2.15"/>
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<dependency org="javax.mail" name="mail" rev="1.4.4"/>
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<dependency org="colt" name="colt" rev="1.2.0"/>
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<dependency org="it.unimi.dsi" name="fastutil" rev="6.5.3" />
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<!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
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<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
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<dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
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<!-- Dependencies for reflections mvn repository -->
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<dependency org="org.reflections" name="reflections" rev="0.9.8"/>
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<dependency org="org.slf4j" name="slf4j-log4j12" rev="1.6.1"/>
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<!-- Matrix package from math.nist.gov -->
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<dependency org="gov.nist" name="Jama" rev="1.0.2"/>
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<!-- Dependencies for the graph aligner -->
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<dependency org="net.sf.jgrapht" name="jgrapht" rev="0.8.3"/>
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<!-- Dependencies for the html walker documention -->
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<dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>
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<!-- Commons Dependencies -->
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<dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
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<dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
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<dependency org="commons-lang" name="commons-lang" rev="2.5"/>
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<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
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<dependency org="commons-io" name="commons-io" rev="2.1"/>
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<dependency org="commons-collections" name="commons-collections" rev="3.2.1"/>
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<dependency org="org.apache.commons" name="commons-math" rev="2.2"/>
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<!-- Lucene core utilities -->
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<!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->
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<!-- Dependencies for LSF, DRMAA, and other C libraries -->
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<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
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<!-- Dependencies for amazon.com S3 support -->
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<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>
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<!-- Dependencies for GridEngine -->
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<dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
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<!-- Scala dependancies -->
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<dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
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<dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
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<!-- testing and evaluation dependencies -->
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<dependency org="org.testng" name="testng" rev="6.8"/>
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<dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
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<dependency org="com.google.caliper" name="caliper" rev="0.5-rc1"/>
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<dependency org="com.google.inject" name="guice" rev="3.0"/>
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<!-- Contracts for Java and dependencies -->
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<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
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<dependency org="asm" name="asm-all" rev="3.3.1"/>
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<!-- POI, for reading pipeline files -->
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<dependency org="org.apache.poi" name="poi" rev="3.8-beta3"/>
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<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3"/>
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<!-- snpEff annotator for pipelines -->
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<dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5"/>
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<!-- MongoDB for the GXDB project -->
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<dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
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<!-- GSON and HTTP for talking to the REST API on Vanilla Forums -->
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<dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
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<dependency org="org.apache.httpcomponents" name="httpclient" rev="4.1.1"/>
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<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
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<exclude org="javax.servlet"/>
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<exclude org="javax.jms"/>
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<exclude org="com.sun.*"/>
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</dependencies>
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</ivy-module>
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@ -1,9 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package name="Aligner">
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<executable name="Aligner">
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<dependencies>
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<!-- BWA/C aligner implementation -->
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<class name="org.broadinstitute.sting.alignment.bwa.c.BWACAligner" />
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</dependencies>
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</executable>
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</package>
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@ -1,220 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
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<xsl:variable name="ant.basedir" select="'${basedir}'" />
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<xsl:variable name="sting.dir" select="'${sting.dir}/'" />
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<xsl:variable name="classpath" select="'${sting.dir}/staging:${additional.jars}'" />
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<xsl:variable name="dist.dir" select="'${sting.dir}/dist'" />
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<xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
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<xsl:variable name="package.basename" select="'${package.basename}'" />
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<xsl:variable name="package.dir" select="'${package.dir}'" />
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<xsl:variable name="package.filename" select="'${package.filename}'" />
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<xsl:variable name="resources.dir" select="'${package.dir}/resources'" />
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<xsl:template match="package">
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<xsl:output method="xml" indent="yes"/>
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<project name="{@name}" default="package">
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<property name="sting.dir" value="{$ant.basedir}" />
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<!-- Read version information out of the xml file -->
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<xsl:choose>
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<xsl:when test="version/@property">
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<xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
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<property file="{$staging.dir}/{version/@file}" />
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<property name="package.basename" value="{concat(@name,'-',$version.property)}" />
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</xsl:when>
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<xsl:otherwise>
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<property name="package.basename" value="{@name}" />
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</xsl:otherwise>
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</xsl:choose>
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<property name="package.dir" value="{concat($dist.dir,'/packages/',$package.basename)}" />
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<property name="package.filename" value="{concat($package.basename,'.tar.bz2')}" />
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<target name="package">
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<!-- Verify that all classes specified are present -->
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<xsl:for-each select="//class">
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<available property="is.{@name}.present" classpath="{$classpath}" classname="{@name}"/>
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<fail message="Class {@name} not found" unless="is.{@name}.present" />
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</xsl:for-each>
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<xsl:for-each select="//resource-bundle">
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<available property="is.{@file}.present" file="{$staging.dir}/{@file}"/>
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<fail message="Resource bundle {@file} not found" unless="is.{@file}.present" />
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</xsl:for-each>
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<!-- Verify that all files specified are present -->
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<xsl:for-each select="//dependencies/file">
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<xsl:choose>
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<xsl:when test="@name">
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<available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="file"/>
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<fail message="File dependency {@name} not found" unless="is.{@name}.present" />
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</xsl:when>
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<xsl:when test="@path">
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<available property="is.{@path}.present" file="{$staging.dir}/{@path}" type="file"/>
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<fail message="File dependency {@path} not found" unless="is.{@path}.present" />
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</xsl:when>
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<xsl:otherwise>
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<fail message="File dependency must specify a name or a path"/>
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</xsl:otherwise>
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</xsl:choose>
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</xsl:for-each>
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<xsl:for-each select="//dependencies/dir">
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<available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="dir"/>
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<fail message="Directory {@name} not found" unless="is.{@name}.present" />
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</xsl:for-each>
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<!-- Create an output directory for the package -->
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<mkdir dir="{$package.dir}"/>
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<!-- Create the executable sections -->
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<xsl:apply-templates select="executable" />
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<!-- Add in other modules -->
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<xsl:for-each select="modules/module">
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<xsl:apply-templates select="document(@file)/package/executable" />
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</xsl:for-each>
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<!-- Include various resource files explicitly specified in this file and in all other modules -->
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<xsl:apply-templates select="resources" />
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<xsl:for-each select="//modules/module">
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<xsl:apply-templates select="document(@file)/package/resources" />
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</xsl:for-each>
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<!-- Bundle the package into a single zip file -->
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<tar destfile="{$dist.dir}/packages/{$package.filename}" compression="bzip2">
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<fileset dir="{$dist.dir}/packages" includes="{$package.basename}/**"/>
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</tar>
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</target>
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<target name="release">
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<xsl:for-each select="release/executable">
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<copy todir="{@directory}/{$package.basename}"><fileset dir="{$package.dir}" /></copy>
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<xsl:if test="@symlink">
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<symlink link="{@directory}/{@symlink}" resource="{$package.basename}" overwrite="true" />
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</xsl:if>
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</xsl:for-each>
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<xsl:for-each select="release/archive">
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<copy file="{$dist.dir}/packages/{$package.filename}" todir="{@directory}" />
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<xsl:if test="@symlink">
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<symlink link="{@directory}/{@symlink}" resource="{$package.filename}" overwrite="true" />
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</xsl:if>
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</xsl:for-each>
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</target>
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</project>
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</xsl:template>
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<!-- Create a symlink for the given file in the given target directory -->
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<xsl:template name="symlink">
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<xsl:param name="file.name" />
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<xsl:param name="target.dir" />
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<xsl:variable name="short.name">
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<xsl:call-template name="get-short-name">
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<xsl:with-param name="string" select="$file.name" />
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</xsl:call-template>
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</xsl:variable>
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<xsl:variable name="full.path">
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<xsl:call-template name="get-full-path">
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<xsl:with-param name="working-dir" select="$sting.dir"/>
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<xsl:with-param name="file" select="$file.name" />
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</xsl:call-template>
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</xsl:variable>
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<available property="is.{$short.name}.present" file="{$file.name}"/>
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<fail message="File {$file.name} not found" unless="is.{$short.name}.present" />
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<delete file="{$target.dir}/{$short.name}" />
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<symlink link="{$target.dir}/{$short.name}" resource="{$full.path}" overwrite="true" />
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</xsl:template>
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<!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
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<xsl:template match="executable">
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<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
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<jar jarfile="{$package.dir}/{@name}.jar">
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<classfileset dir="{$staging.dir}">
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<root classname="{main-class/@name}"/>
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</classfileset>
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<xsl:for-each select="resource-bundle">
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<fileset file="{$staging.dir}/{@file}" />
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</xsl:for-each>
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<xsl:for-each select="modules/module">
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<xsl:apply-templates select="document(@file)/package/executable/dependencies" />
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</xsl:for-each>
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<xsl:apply-templates select="dependencies" />
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<manifest>
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<attribute name="Main-Class" value="{main-class/@name}"/>
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</manifest>
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</jar>
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</xsl:template>
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<!-- Transform a resource file into a symlink operation -->
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<xsl:template match="resources">
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<xsl:for-each select="file">
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<mkdir dir="{$resources.dir}"/>
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<xsl:call-template name="symlink">
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<xsl:with-param name="file.name" select="@name" />
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<xsl:with-param name="target.dir" select="$resources.dir" />
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</xsl:call-template>
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</xsl:for-each>
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</xsl:template>
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<!-- Transform a dependency list into a fileset for embedding in a jar -->
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<xsl:template match="dependencies">
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<classfileset dir="{$staging.dir}">
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<xsl:for-each select="package">
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<rootfileset dir="{$staging.dir}" includes="{concat(translate(@name,'.','/'),'/','*.class')}" />
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</xsl:for-each>
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<xsl:for-each select="class">
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<root classname="{@name}" />
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</xsl:for-each>
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</classfileset>
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<xsl:for-each select="file">
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<xsl:choose>
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<xsl:when test="@name">
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<fileset file="{$staging.dir}/{@name}" />
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</xsl:when>
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<xsl:when test="@path">
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<fileset dir="{$staging.dir}">
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<xsl:attribute name="includes">
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<xsl:value-of select="@path"/>
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</xsl:attribute>
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</fileset>
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</xsl:when>
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</xsl:choose>
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</xsl:for-each>
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<xsl:for-each select="dir">
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<xsl:variable name="includes">
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<xsl:choose>
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<xsl:when test="@includes = ''">
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<xsl:value-of select="concat(@name,'/**')"/>
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</xsl:when>
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<xsl:otherwise>
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<xsl:value-of select="concat(@name,'/',@includes)"/>
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</xsl:otherwise>
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</xsl:choose>
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</xsl:variable>
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<fileset dir="{$staging.dir}" includes="{$includes}"/>
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</xsl:for-each>
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</xsl:template>
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<!-- Determine the short name (filename w/o directory structure of the given filename -->
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<xsl:template name="get-short-name">
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<xsl:param name="string"/>
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<xsl:choose>
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<xsl:when test="contains($string,'/')">
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<xsl:call-template name="get-short-name">
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<xsl:with-param name="string" select="substring-after($string,'/')" />
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</xsl:call-template>
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</xsl:when>
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<xsl:otherwise><xsl:value-of select="$string"/></xsl:otherwise>
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</xsl:choose>
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</xsl:template>
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<!-- Determine the full path of the given filename. Take into account absolute / relative paths -->
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<xsl:template name="get-full-path">
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<xsl:param name="working-dir"/>
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<xsl:param name="file"/>
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<xsl:choose>
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<xsl:when test="starts-with($file,'/')"><xsl:value-of select="$file"/></xsl:when>
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<xsl:otherwise><xsl:value-of select="concat($working-dir,$file)"/></xsl:otherwise>
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</xsl:choose>
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</xsl:template>
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</xsl:stylesheet>
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@ -1,62 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!--
|
||||
~ 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">
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<executable name="GATKEngine">
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<dependencies>
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<!-- Package everything in org.broadinstitute.sting -->
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<package name="org.broadinstitute.sting.**" />
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<!-- Tribble codecs -->
|
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<package name="org.broad.tribble.**" />
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<!-- The variant package (VCF, BCF, and VariantContext) -->
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<package name="org.broadinstitute.variant.**" />
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<!-- Workaround - depend on the logger impl required by JEXL -->
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<package name="org.apache.commons.logging.impl" />
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<!-- R packages -->
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<dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
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<!-- All R scripts in org.broadinstitute.sting -->
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<dir name="org/broadinstitute/sting" includes="**/*.R" />
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<!-- Resources in org.broadinstitute.sting -->
|
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<dir name="org/broadinstitute/sting" includes="**/resources/*" />
|
||||
<dir name="org/broadinstitute/sting" includes="**/templates/*" />
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<!-- The GATK public key -->
|
||||
<file path="GATK_public.key" />
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</dependencies>
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||||
</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/qc/Pileup.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/CheckPileup.java" />
|
||||
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java" />
|
||||
</resources>
|
||||
</package>
|
||||
|
|
@ -1,40 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!--
|
||||
~ Copyright (c) 2012, 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.
|
||||
-->
|
||||
|
||||
<!-- The full release of the GATK contains both public and protected tools (but nothing from private) -->
|
||||
<package name="GenomeAnalysisTK">
|
||||
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
|
||||
<executable name="GenomeAnalysisTK">
|
||||
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
|
||||
<resource-bundle file="StingText.properties" />
|
||||
<modules>
|
||||
<module file="GATKEngine.xml"/>
|
||||
</modules>
|
||||
</executable>
|
||||
<release>
|
||||
<executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
|
||||
<archive directory="/humgen/gsa-hpprojects/GATK/bin" symlink="GenomeAnalysisTK-latest.tar.bz2" />
|
||||
</release>
|
||||
</package>
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<package name="picard-private-parts">
|
||||
<executable name="picard-private-parts">
|
||||
<dependencies>
|
||||
<class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
|
||||
<class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
|
||||
<class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />
|
||||
</dependencies>
|
||||
</executable>
|
||||
</package>
|
||||
|
|
@ -1,41 +0,0 @@
|
|||
<?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.
|
||||
-->
|
||||
|
||||
<!-- The full release of Queue contains both public and protected tools (but nothing from private) -->
|
||||
<package name="Queue">
|
||||
<version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
|
||||
<executable name="Queue">
|
||||
<main-class name="org.broadinstitute.sting.queue.QCommandLine" />
|
||||
<resource-bundle file="StingText.properties" />
|
||||
<modules>
|
||||
<module file="QueueEngine.xml"/>
|
||||
<module file="GATKEngine.xml"/>
|
||||
</modules>
|
||||
</executable>
|
||||
<release>
|
||||
<executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
|
||||
<archive directory="/humgen/gsa-hpprojects/Queue/bin" symlink="Queue-latest.tar.bz2" />
|
||||
</release>
|
||||
</package>
|
||||
|
|
@ -1,78 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!--
|
||||
~ Copyright (c) 2012, 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="QueueEngine">
|
||||
<executable name="QueueEngine">
|
||||
<dependencies>
|
||||
<!-- Queue -->
|
||||
<package name="org.broadinstitute.sting.queue.**" />
|
||||
|
||||
<!-- Pipeline + Utils -->
|
||||
<package name="org.broadinstitute.sting.pipeline.**" />
|
||||
<package name="org.broadinstitute.sting.utils.**" />
|
||||
|
||||
<!-- Scala -->
|
||||
<package name="scala.**" />
|
||||
|
||||
<!-- Picard -->
|
||||
<package name="net.sf.picard.**" />
|
||||
<package name="edu.mit.broad.picard.**" />
|
||||
|
||||
<!-- JavaMail -->
|
||||
<package name="javax.activation.**" />
|
||||
<package name="javax.mail.**" />
|
||||
<package name="com.sun.activation.**" />
|
||||
<package name="com.sun.mail.**" />
|
||||
<file path="META-INF/javamail.charset.map" />
|
||||
<file path="META-INF/javamail.default.address.map" />
|
||||
<file path="META-INF/javamail.default.providers" />
|
||||
<file path="META-INF/mailcap" />
|
||||
<file path="META-INF/mailcap.default" />
|
||||
<file path="META-INF/mimetypes.default" />
|
||||
|
||||
<!-- JNA, including embedded native libraries -->
|
||||
<dir name="com/sun/jna" />
|
||||
|
||||
<!-- Contracts for Java -->
|
||||
<package name="com.google.java.contract.**" />
|
||||
|
||||
<!-- snpEff -->
|
||||
<package name="ca.mcgill.mcb.pcingola.**" />
|
||||
<file path="snpEff_genes.ftl" />
|
||||
<file path="snpEff_summary.ftl" />
|
||||
|
||||
<!-- R scripts -->
|
||||
<dir name="org/broadinstitute/sting/queue" includes="**/*.R" />
|
||||
</dependencies>
|
||||
</executable>
|
||||
<resources>
|
||||
<!-- Sample QScripts -->
|
||||
<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala" />
|
||||
<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala" />
|
||||
<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala" />
|
||||
<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala" />
|
||||
<file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala" />
|
||||
</resources>
|
||||
</package>
|
||||
|
|
@ -1 +0,0 @@
|
|||
repository.dir=${ivy.settings.dir}/repository
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
<ivysettings>
|
||||
<properties file="${ivy.settings.dir}/ivysettings.properties"/>
|
||||
<settings defaultResolver="chain"/>
|
||||
<resolvers>
|
||||
<chain name="chain">
|
||||
<filesystem name="projects">
|
||||
<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
|
||||
<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
|
||||
</filesystem>
|
||||
<ibiblio name="maven" root="http://repo1.maven.org/maven2" m2compatible="true" />
|
||||
</chain>
|
||||
</resolvers>
|
||||
</ivysettings>
|
||||
Loading…
Reference in New Issue