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Remove the ability to package GATK/Queue Lite from the build system 

Still need to reconfigure Bamboo to open-source protected, but this
can be done during the 2.4 release freeze.
This commit is contained in:
David Roazen 2013-01-28 02:40:18 -05:00
parent 3744d1a596
commit 1599c9a20e
3 changed files with 0 additions and 106 deletions
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27
build.xml
View File

@ -873,10 +873,6 @@
<property name="executable" value="GenomeAnalysisTK" />
</target>
<target name="init.executable.gatklite" depends="init.build.publiconly, init.javaonly">
<property name="executable" value="GenomeAnalysisTKLite" />
</target>
<target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
<property name="executable" value="Queue" />
</target>
@ -885,10 +881,6 @@
<property name="executable" value="Queue" />
</target>
<target name="init.executable.queuelite" depends="init.build.publiconly, init.javaandscala">
<property name="executable" value="QueueLite" />
</target>
<target name="require.executable">
<condition property="no.executable.defined">
<or>
@ -939,15 +931,10 @@
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="package.gatk.full" depends="init.executable.gatkfull,package" />
<target name="package.gatk.lite" depends="init.executable.gatklite,package" />
<target name="package.queue.all" depends="init.executable.queueall,package" />
<target name="package.queue.full" depends="init.executable.queuefull,package" />
<target name="package.queue.lite" depends="init.executable.queuelite,package" />
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
<target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
@ -956,13 +943,8 @@
<!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="release.gatk.full" depends="package.gatk.full,release" />
<target name="release.gatk.lite" depends="package.gatk.lite,release" />
<target name="release.queue.full" depends="package.queue.full,release" />
<target name="release.queue.lite" depends="package.queue.lite,release" />
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
<target name="build-picard-private" depends="resolve">
@ -1006,14 +988,10 @@
<!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
<target name="mvninstall.gatk.lite" depends="package.gatk.lite,mvninstall" />
<target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
<target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
<target name="mvninstall.queue.lite" depends="package.queue.lite,mvninstall" />
<!-- ******************************************************************************** -->
<!-- Clean -->
<!-- ******************************************************************************** -->
@ -1363,13 +1341,8 @@
<!-- Order of the dependencies is significant in the *.release.tests targets -->
<target name="gatkfull.binary.release.tests" depends="init.usecontracts,package.gatk.full,init.testgatkjar,unittest,integrationtest" />
<target name="gatklite.binary.release.tests" depends="init.usecontracts,package.gatk.lite,init.testgatkjar,unittest,integrationtest" />
<target name="queuefull.binary.release.tests" depends="init.usecontracts,package.queue.full,init.testqueuejar,pipelinetest" />
<target name="queuelite.binary.release.tests" depends="init.usecontracts,package.queue.lite,init.testqueuejar,pipelinetest" />
<!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
<target name="unittest" depends="test.compile,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">

39
public/packages/GenomeAnalysisTKLite.xml
View File

@ -1,39 +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 lite release of the GATK contains only public tools (nothing from protected or private) -->
<package name="GenomeAnalysisTKLite">
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
<executable name="GenomeAnalysisTKLite">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<modules>
<module file="GATKEngine.xml"/>
</modules>
</executable>
<release>
<archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTKLite-latest.tar.bz2" />
</release>
</package>

40
public/packages/QueueLite.xml
View File

@ -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 lite release of Queue contains only public tools (nothing from protected or private) -->
<package name="QueueLite">
<version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
<executable name="QueueLite">
<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>
<archive directory="/web/ftp/pub/gsa/Queue" symlink="QueueLite-latest.tar.bz2" />
</release>
</package>