From 1599c9a20e3c25faa899f496d76f7344c38e1e9b Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Mon, 28 Jan 2013 02:40:18 -0500
Subject: [PATCH] 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.
---
 build.xml                                | 27 ----------------
 public/packages/GenomeAnalysisTKLite.xml | 39 -----------------------
 public/packages/QueueLite.xml            | 40 ------------------------
 3 files changed, 106 deletions(-)
 delete mode 100644 public/packages/GenomeAnalysisTKLite.xml
 delete mode 100644 public/packages/QueueLite.xml

diff --git a/build.xml b/build.xml
index 2dfff0cc2..e92e41c10 100644
--- a/build.xml
+++ b/build.xml
@@ -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}">
diff --git a/public/packages/GenomeAnalysisTKLite.xml b/public/packages/GenomeAnalysisTKLite.xml
deleted file mode 100644
index b2f73434c..000000000
--- a/public/packages/GenomeAnalysisTKLite.xml
+++ /dev/null
@@ -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>
diff --git a/public/packages/QueueLite.xml b/public/packages/QueueLite.xml
deleted file mode 100644
index 0ead68fb0..000000000
--- a/public/packages/QueueLite.xml
+++ /dev/null
@@ -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>