diff --git a/pom.xml b/pom.xml
new file mode 100644
index 000000000..787bd5d31
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,733 @@
+
+
+ 4.0.0
+
+
+
+
+ org.broadinstitute.sting
+ sting-root
+ 2.6-SNAPSHOT
+ public/sting-root
+
+
+ sting-aggregator
+ pom
+ Sting Aggregator
+
+
+ public
+
+
+
+
+ ${project.basedir}
+ StingText.properties
+ false
+
+ -build-timestamp "${maven.build.timestamp}"
+ package
+ true
+ ${sting.packagecommittests.skipped}
+ ${sting.packagecommittests.skipped}
+ ${sting.packagecommittests.skipped}
+ true
+
+
+
+
+ com.sun
+ tools
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-clean-plugin
+
+
+
+
+ gatkdocs
+
+
+ ${basedir}
+
+ javadoc.sh
+ options
+ packages
+
+
+
+
+ ${basedir}
+
+ dependency-reduced-pom.xml
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+ unpack-direct-dependencies
+
+ unpack-dependencies
+
+ none
+
+ true
+ ${project.build.outputDirectory}
+ jar
+ system
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+
+
+ copy-resource-bundle-log4j
+
+ copy-resources
+
+ none
+
+ ${project.reporting.outputDirectory}/apidocs
+
+
+ ${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+
+
+ extract-resource-bundle
+
+ javadoc
+
+ none
+
+
+ ${resource.bundle.skip}
+ org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet
+
+ ${project.build.outputDirectory}
+
+ ${project.groupId}
+
+ gatk-framework
+ ${project.version}
+
+ 2g
+ false
+ true
+ -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} -out ${project.build.outputDirectory}/${resource.bundle.path}
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-compiler-plugin
+
+ none
+
+ com.google.java.contract.core.apt.AnnotationProcessor
+
+
+
+ ${java.home}/lib/rt.jar:${java.home}/lib/jce.jar
+
+
+
+
+ default-compile
+ none
+
+
+ default-testCompile
+ none
+
+
+
+ compile-package-info
+
+ compile
+
+ compile
+
+
+ -Xpkginfo:always
+
+
+ **/package-info.java
+
+
+
+
+
+ compile-java
+
+ compile
+
+ compile
+
+
+
+ **/package-info.java
+
+
+
+
+
+ testCompile-java
+
+ testCompile
+
+ test-compile
+
+
+
+
+
+ org.scala-tools
+ maven-scala-plugin
+
+
+
+ compile
+ testCompile
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+ default-jar
+ ${sting.jar.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-shade-plugin
+
+
+ sting-executable
+
+ shade
+
+ none
+
+ true
+
+
+ org.broadinstitute.sting:gsalib:tar.gz:*
+ org.broadinstitute.sting:*:tar.bz2:example-resources
+
+
+
+
+
+ ${app.main.class}
+
+
+
+ ${resource.bundle.path}
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ example-resources
+
+ single
+
+ none
+
+
+ src/main/assembly/example-resources.xml
+
+
+
+
+ binary-dist
+
+ single
+
+ none
+
+
+ src/main/assembly/binary-dist.xml
+
+
+
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-public-testdata
+
+ link
+
+ none
+
+
+
+ ${basedir}/public/testdata
+ ${sting.basedir}/public/gatk-framework/src/test/resources
+
+
+
+
+
+ unlink-public-testdata
+
+ unlink
+
+ none
+
+
+
+ ${basedir}/public/testdata
+ ${sting.basedir}/public/gatk-framework/src/test/resources
+
+
+
+
+
+ link-private-testdata
+
+ link
+
+ none
+
+
+
+ ${basedir}/private/testdata
+ ${sting.basedir}/private/gatk-private/src/test/resources
+
+
+
+
+
+ unlink-private-testdata
+
+ unlink
+
+ none
+
+
+
+ ${basedir}/private/testdata
+ ${sting.basedir}/private/gatk-private/src/test/resources
+
+
+
+
+
+ link-public-qscript
+
+ link
+
+ none
+
+
+
+ ${basedir}/public/scala/qscript
+ ${sting.basedir}/public/queue-framework/src/main/qscripts
+
+
+
+
+
+ unlink-public-qscript
+
+ unlink
+
+ none
+
+
+
+ ${basedir}/public/scala/qscript
+ ${sting.basedir}/public/queue-framework/src/main/qscripts
+
+
+
+
+
+ link-private-qscript
+
+ link
+
+ none
+
+
+
+ ${basedir}/private/scala/qscript
+ ${sting.basedir}/private/queue-private/src/main/qscripts
+
+
+
+
+
+ unlink-private-qscript
+
+ unlink
+
+ none
+
+
+
+ ${basedir}/private/scala/qscript
+ ${sting.basedir}/private/queue-private/src/main/qscripts
+
+
+
+
+
+ link-git-release
+
+ link
+
+ none
+
+
+
+ ${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2
+ ${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-invoker-plugin
+
+ true
+ false
+ ${sting.basedir}/public/package-tests/pom.xml
+ true
+ true
+ ${sting.basedir}/${maven.repo.local}
+
+ ${test}
+ ${it.test}
+ false
+ false
+ ${sting.packagetests.artifactId}
+ ${project.build.testOutputDirectory}
+ ${project.basedir}
+ ${sting.pipelinetests.run}
+ ${maven.surefire.debug}
+ ${maven.failsafe.debug}
+
+
+
+
+ package-unittests
+
+ run
+
+
+
+ test
+
+
+ unittests
+
+ ${sting.packageunittests.skipped}
+
+ ${sting.packageunittests.skipped}
+
+
+
+
+ package-integrationtests
+
+ integration-test
+ verify
+
+
+
+ verify
+
+
+ integrationtests
+
+ ${sting.packageintegrationtests.skipped}
+
+ ${sting.packageintegrationtests.skipped}
+
+
+
+
+ package-pipelinetests
+
+ integration-test
+ verify
+
+
+
+ verify
+
+
+ integrationtests
+
+ ${sting.packagepipelinetests.skipped}
+
+ ${sting.packagepipelinetests.skipped}
+
+
+
+
+ package-largescaletests
+
+ integration-test
+ verify
+
+
+
+ verify
+
+
+ integrationtests
+
+ ${sting.packagelargescaletests.skipped}
+
+ ${sting.packagelargescaletests.skipped}
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-install-plugin
+ 2.5
+
+
+ install-package
+
+ install-file
+
+ none
+
+ true
+ ${project.groupId}
+ ${project.artifactId}
+ ${project.version}
+ ${project.packaging}
+ ${project.build.directory}/${project.build.finalName}.${project.packaging}
+
+
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-failsafe-plugin
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-public-testdata
+ process-test-resources
+
+
+ unlink-public-testdata
+ clean
+
+
+
+
+ org.apache.maven.plugins
+ maven-clean-plugin
+
+
+ com.google.code.sortpom
+ maven-sortpom-plugin
+
+
+ package-tests
+
+ sort
+
+ verify
+ false
+
+ public/package-tests/pom.xml
+
+
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+ 2.9.1
+
+
+
+
+
+
+ generate-gatk-docs
+
+ aggregate
+
+
+ false
+
+ org.broadinstitute.sting.utils.help.GATKDoclet
+
+ ${project.groupId}
+ gatk-package
+ ${project.version}
+
+ false
+ true
+ private
+
+ ../..
+ -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden}
+
+ false
+
+
+
+
+
+
+
+
+
+
+ protected
+
+
+ ${basedir}/protected/pom.xml
+
+
+
+ protected
+
+
+
+
+
+ private
+
+
+ ${basedir}/private/pom.xml
+
+
+
+ private
+
+
+
+
+
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
new file mode 100644
index 000000000..d3e50eec9
--- /dev/null
+++ b/protected/gatk-protected/pom.xml
@@ -0,0 +1,144 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ gatk-protected
+ jar
+ GATK Protected
+
+
+ ${project.basedir}/../..
+ gatk-package
+
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+
+
+
+ net.sf.jgrapht
+ jgrapht
+
+
+
+ gov.nist
+ Jama
+
+
+
+ it.unimi.dsi
+ fastutil
+
+
+
+ ${project.groupId}
+ sting-utils
+ ${project.version}
+ test-jar
+ test
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+ test-jar
+ test
+
+
+
+ org.testng
+ testng
+ test
+
+
+ com.google.caliper
+ caliper
+ test
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+
+
+ copy-resource-bundle-log4j
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+
+
+ extract-resource-bundle
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-invoker-plugin
+
+
+ package-unittests
+
+
+ package-integrationtests
+
+
+ package-largescaletests
+
+
+ package-pipelinetests
+
+
+
+
+
+
+
+
+ private
+
+
+ ${basedir}/../../private/gatk-private/pom.xml
+
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-private-testdata
+ process-test-resources
+
+
+ unlink-private-testdata
+ clean
+
+
+
+
+
+
+
+
+
diff --git a/protected/pom.xml b/protected/pom.xml
new file mode 100644
index 000000000..a7fb4863f
--- /dev/null
+++ b/protected/pom.xml
@@ -0,0 +1,24 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-root
+ 2.6-SNAPSHOT
+ ../public/sting-root
+
+
+ sting-protected
+ pom
+ Sting Protected
+
+
+ gatk-protected
+
+
+
+ ${project.basedir}/..
+
+
+
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
new file mode 100644
index 000000000..37739bfda
--- /dev/null
+++ b/public/external-example/pom.xml
@@ -0,0 +1,257 @@
+
+ 4.0.0
+
+
+ org.mycompany.app
+ external-example
+ jar
+ 1.0-SNAPSHOT
+ external-example
+
+
+ 2.6-SNAPSHOT
+
+ ../..
+ UTF-8
+ UTF-8
+ yyyy/MM/dd HH:mm:ss
+
+
+
+
+ sting.public.repo.local
+ Sting Public Local Repository
+ file:${sting.basedir}/public/repo
+
+
+
+
+
+ org.broadinstitute.sting
+ gatk-framework
+ ${sting.version}
+
+
+
+
+ org.broadinstitute.sting
+ sting-utils
+ ${sting.version}
+ test-jar
+ test
+
+
+
+ org.broadinstitute.sting
+ gatk-framework
+ ${sting.version}
+ test-jar
+ test
+
+
+
+ org.testng
+ testng
+ 6.8
+ test
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+ 2.8
+
+
+ unpack
+ process-resources
+
+ unpack
+
+
+
+
+ org.broadinstitute.sting
+ gatk-framework
+ ${sting.version}
+ example-resources
+ tar.bz2
+ ${project.build.outputDirectory}
+
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+ 2.9.1
+
+
+ extract-resource-bundle
+
+ javadoc
+
+ prepare-package
+
+ org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet
+
+ ${project.build.outputDirectory}
+
+ org.broadinstitute.sting
+
+ gatk-framework
+ ${sting.version}
+
+ 2g
+ false
+ true
+ -build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/StingText.properties
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-shade-plugin
+ 2.1
+
+
+ package
+
+ shade
+
+
+ true
+
+
+
+ commons-logging:commons-logging
+
+ **
+
+
+
+ org.broad:tribble
+
+ **
+
+
+
+ org.broadinstitute:variant
+
+ **
+
+
+
+
+
+
+ org.broadinstitute.sting:gsalib:tar.gz:*
+ org.broadinstitute.sting:*:tar.bz2:example-resources
+
+
+
+
+
+ org.broadinstitute.sting.gatk.CommandLineGATK
+
+
+
+ StingText.properties
+
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-surefire-plugin
+ 2.16
+
+
+ true
+
+
+ false
+
+
+
+
+ default-test
+ none
+
+
+
+ unit-tests
+
+ test
+
+
+ false
+
+ **/*Test.class
+
+
+ **/*IntegrationTest.class
+
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-failsafe-plugin
+ 2.16
+
+
+ true
+
+
+ false
+
+
+
+
+ integration-tests
+
+ integration-test
+ verify
+
+
+
+ false
+
+ **/*IntegrationTest.class
+
+
+
+
+
+
+
+
+
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
new file mode 100644
index 000000000..f4443a2f6
--- /dev/null
+++ b/public/gatk-framework/pom.xml
@@ -0,0 +1,142 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ gatk-framework
+ jar
+ GATK Framework
+
+
+ ${project.basedir}/../..
+ gatk-package
+
+
+
+
+ ${project.groupId}
+ sting-utils
+ ${project.version}
+
+
+
+ ${project.groupId}
+ sting-utils
+ ${project.version}
+ test-jar
+ test
+
+
+
+ org.testng
+ testng
+ test
+
+
+ com.google.caliper
+ caliper
+ test
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ example-resources
+ generate-resources
+
+
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+
+
+ copy-resource-bundle-log4j
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+
+
+ extract-resource-bundle
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+
+ test-jar
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-invoker-plugin
+
+
+ package-unittests
+
+
+ package-integrationtests
+
+
+ package-largescaletests
+
+
+ package-pipelinetests
+
+
+
+
+
+
+
+
+ private
+
+
+ ${basedir}/../../private/gatk-private/pom.xml
+
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-private-testdata
+ process-test-resources
+
+
+ unlink-private-testdata
+ clean
+
+
+
+
+
+
+
+
+
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
new file mode 100644
index 000000000..4f5a70268
--- /dev/null
+++ b/public/gatk-package/pom.xml
@@ -0,0 +1,155 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ gatk-package
+ jar
+ GATK Package
+
+
+ ${project.basedir}/../..
+ prepare-package
+ package
+ org.broadinstitute.sting.gatk.CommandLineGATK
+ GenomeAnalysisTK
+
+
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+
+
+
+ org.broad
+ tribble
+
+
+
+ org.broadinstitute
+ variant
+
+
+
+ commons-logging
+ commons-logging
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+ example-resources
+ tar.bz2
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+ unpack-direct-dependencies
+ ${sting.unpack.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-shade-plugin
+
+
+ sting-executable
+ ${sting.shade.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ binary-dist
+ ${sting.shade.phase}
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-git-release
+ ${sting.shade.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-install-plugin
+
+
+ default-install
+ none
+
+
+ install-package
+ install
+
+
+
+
+
+
+
+
+
+ protected
+
+
+ ${basedir}/../../protected/gatk-protected/pom.xml
+
+
+
+
+ ${project.groupId}
+ gatk-protected
+ ${project.version}
+ true
+
+
+
+
+ private
+
+
+ ${basedir}/../../private/gatk-private/pom.xml
+
+
+
+
+ ${project.groupId}
+ gatk-private
+ ${project.version}
+ true
+
+
+
+
+
+
diff --git a/public/gatk-queue-extgen/pom.xml b/public/gatk-queue-extgen/pom.xml
new file mode 100644
index 000000000..9aba4f1a4
--- /dev/null
+++ b/public/gatk-queue-extgen/pom.xml
@@ -0,0 +1,29 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ gatk-queue-extgen
+ jar
+ Queue GATK ExtGen
+ Queue GATK Extensions Generator
+
+
+ ${project.basedir}/../..
+
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+
+
+
+
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
new file mode 100644
index 000000000..a51a985f1
--- /dev/null
+++ b/public/gsalib/pom.xml
@@ -0,0 +1,45 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ gsalib
+ pom
+ Sting GSALib
+
+
+ ${project.basedir}/../..
+ org/broadinstitute/sting/utils/R
+ gsalib.tar.gz
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ gsalib-assembly
+
+ single
+
+ generate-resources
+
+ false
+
+ src/assembly/gsalib.xml
+
+
+
+
+
+
+
+
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
new file mode 100644
index 000000000..3d1bc1136
--- /dev/null
+++ b/public/package-tests/pom.xml
@@ -0,0 +1,158 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-root
+ 2.6-SNAPSHOT
+ ../sting-root
+
+
+ sting-package-tests
+ pom
+ Sting Package Tests
+
+
+ ${project.basedir}/../..
+
+
+
+
+
+ ${project.groupId}
+ ${sting.packagetests.artifactId}
+ ${project.version}
+
+
+
+
+ com.sun
+ tools
+
+
+
+ com.google.code.cofoja
+ cofoja
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+ test-jar
+ test
+
+
+
+ org.testng
+ testng
+ test
+
+
+
+ com.google.caliper
+ caliper
+ test
+
+
+
+
+ ${sting.packagetests.basedir}/target
+
+
+
+
+ unittests
+
+
+
+
+ org.apache.maven.plugins
+ maven-surefire-plugin
+
+ ${sting.packagetests.basedir}
+ ${sting.packagetests.basedir}
+ ${project.build.outputDirectory}/ignored_by_package_test
+ ${sting.packagetests.testClasses}
+
+ org.broadinstitute.sting:.*
+
+
+
+
+
+ unit-tests
+
+ test
+
+
+ ${sting.packageunittests.skipped}
+
+
+
+
+
+
+
+
+
+ integrationtests
+
+
+
+
+ org.apache.maven.plugins
+ maven-failsafe-plugin
+
+ ${sting.packagetests.basedir}
+ ${sting.packagetests.basedir}
+ ${project.build.outputDirectory}/ignored_by_package_test
+ ${sting.packagetests.testClasses}
+
+ org.broadinstitute.sting:.*
+
+
+
+
+ integration-tests
+
+ verify
+
+
+
+ ${sting.packageintegrationtests.skipped}
+
+
+
+ pipeline-tests
+
+ verify
+
+
+
+ ${sting.packagepipelinetests.skipped}
+
+
+
+ large-scale-tests
+
+ verify
+
+
+
+ ${sting.packagelargescaletests.skipped}
+
+
+
+
+
+
+
+
+
+
+
diff --git a/public/pom.xml b/public/pom.xml
new file mode 100644
index 000000000..e3173c35b
--- /dev/null
+++ b/public/pom.xml
@@ -0,0 +1,46 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-root
+ 2.6-SNAPSHOT
+ sting-root
+
+
+ sting-public
+ pom
+ Sting Public
+
+
+ sting-root
+ gsalib
+ sting-utils
+ gatk-framework
+ gatk-package
+
+
+
+
+ ${project.basedir}/..
+
+
+
+
+
+ queue
+
+
+ !disable.queue
+
+
+
+ gatk-queue-extgen
+ queue-framework
+ queue-package
+
+
+
+
+
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
new file mode 100644
index 000000000..8ccc7f351
--- /dev/null
+++ b/public/queue-framework/pom.xml
@@ -0,0 +1,267 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ queue-framework
+ jar
+ Queue Framework
+
+
+ ${project.basedir}/../..
+ ${project.build.directory}/generated-sources/gatk-extensions
+ false
+ queue-package
+
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+
+
+ org.scala-lang
+ scala-compiler
+
+
+ log4j
+ log4j
+
+
+ net.sf.jgrapht
+ jgrapht
+
+
+ org.apache.commons
+ commons-email
+
+
+ javax.mail
+ mail
+
+
+
+ ${project.groupId}
+ gatk-queue-extgen
+ ${project.version}
+ runtime
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+ test-jar
+ test
+
+
+
+ org.testng
+ testng
+ test
+
+
+
+
+
+
+ org.codehaus.mojo
+ exec-maven-plugin
+
+
+ generate-gatk-extensions
+
+ exec
+
+ generate-sources
+
+ ${sting.generate-gatk-extensions.skipped}
+ java
+
+ -classpath
+
+ org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator
+ -l
+ WARN
+ -outDir
+ ${gatk.extensions.sources}
+
+
+
+
+
+
+ org.codehaus.mojo
+ build-helper-maven-plugin
+
+
+ add-gatk-extensions
+
+ add-source
+
+ generate-sources
+
+
+ ${gatk.extensions.sources}
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ example-resources
+ generate-resources
+
+
+
+
+ org.scala-tools
+ maven-scala-plugin
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-public-qscript
+ process-test-resources
+
+
+ unlink-public-qscript
+ clean
+
+
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+
+
+ copy-resource-bundle-log4j
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+
+
+ extract-resource-bundle
+ prepare-package
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+
+ test-jar
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-invoker-plugin
+
+
+ package-unittests
+
+
+ package-integrationtests
+
+
+ package-largescaletests
+
+
+ package-pipelinetests
+
+
+
+
+
+
+
+
+ protected
+
+
+ ${basedir}/../../protected/gatk-protected/pom.xml
+
+
+
+
+ ${project.groupId}
+ gatk-protected
+ ${project.version}
+ true
+
+
+
+
+ private
+
+
+ ${basedir}/../../private/gatk-private/pom.xml
+
+
+
+
+ ${project.groupId}
+ gatk-private
+ ${project.version}
+ true
+
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-private-testdata
+ process-test-resources
+
+
+ unlink-private-testdata
+ clean
+
+
+ link-private-qscript
+ process-test-resources
+
+
+ unlink-private-qscript
+ clean
+
+
+
+
+
+
+
+
+
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
new file mode 100644
index 000000000..1a8bf8b0f
--- /dev/null
+++ b/public/queue-package/pom.xml
@@ -0,0 +1,170 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ queue-package
+ jar
+ Queue Package
+
+
+ ${project.basedir}/../..
+ prepare-package
+ package
+ Queue
+ org.broadinstitute.sting.queue.QCommandLine
+
+
+
+
+
+ ${project.groupId}
+ queue-framework
+ ${project.version}
+
+
+ ${project.groupId}
+ gatk-package
+ ${project.version}
+
+
+
+ org.scala-lang
+ scala-library
+
+
+ org.scala-lang
+ scala-compiler
+
+
+
+ net.sf
+ picard
+
+
+
+ javax.mail
+ mail
+
+
+
+ net.java.dev.jna
+ jna
+
+
+
+ com.google.code.cofoja
+ cofoja
+
+
+
+ net.sf.snpeff
+ snpeff
+
+
+
+ ${project.groupId}
+ gatk-framework
+ ${project.version}
+ example-resources
+ tar.bz2
+
+
+ ${project.groupId}
+ queue-framework
+ ${project.version}
+ example-resources
+ tar.bz2
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+ unpack-direct-dependencies
+ ${sting.unpack.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-shade-plugin
+
+
+ sting-executable
+ ${sting.shade.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+
+
+ binary-dist
+ ${sting.shade.phase}
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+
+
+ link-git-release
+ ${sting.shade.phase}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-install-plugin
+
+
+ default-install
+ none
+
+
+ install-package
+ install
+
+
+
+
+
+
+
+
+
+ private
+
+
+ ${basedir}/../../private/queue-private/pom.xml
+
+
+
+
+ ${project.groupId}
+ queue-private
+ ${project.version}
+ true
+
+
+
+
+
+
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
new file mode 100644
index 000000000..1309175bb
--- /dev/null
+++ b/public/sting-root/pom.xml
@@ -0,0 +1,619 @@
+
+
+ 4.0.0
+
+
+
+ org.broadinstitute.sting
+ sting-root
+ 2.6-SNAPSHOT
+ pom
+ Sting Root
+
+
+ 3.0.4
+
+
+
+ UTF-8
+ ${sourceEncoding}
+ ${sourceEncoding}
+ 1.7
+ 1.7
+ yyyy/MM/dd HH:mm:ss
+ ${project.basedir}/../..
+ true
+ ${sting.committests.skipped}
+ ${sting.committests.skipped}
+ ${sting.committests.skipped}
+ true
+ false
+ 4g
+ -Xmx${test.maxmemory}
+
+
+
+
+
+
+ org.scala-lang
+ scala-compiler
+ 2.10.2
+
+
+ org.scala-lang
+ scala-library
+ 2.10.2
+
+
+ com.google.code.cofoja
+ cofoja
+ 1.0-r139
+
+
+ net.sf
+ sam
+ 1.104.1628
+
+
+ net.sf
+ picard
+ 1.104.1628
+
+
+ edu.mit.broad
+ picard-private-parts
+ 2872
+
+
+ org.broad
+ tribble
+ 1.104.1628
+
+
+ org.broadinstitute
+ variant
+ 1.105.1642
+
+
+ log4j
+ log4j
+ 1.2.15
+
+
+ com.sun.jdmk
+ jmxtools
+
+
+ javax.jms
+ jms
+
+
+ com.sun.jmx
+ jmxri
+
+
+
+
+ javax.mail
+ mail
+ 1.4.4
+
+
+ colt
+ colt
+ 1.2.0
+
+
+ it.unimi.dsi
+ fastutil
+ 6.5.3
+
+
+ org.simpleframework
+ simple-xml
+ 2.0.4
+
+
+ org.apache.bcel
+ bcel
+ 5.2
+
+
+ org.reflections
+ reflections
+ 0.9.8
+
+
+ org.slf4j
+ slf4j-log4j12
+ 1.6.1
+
+
+ gov.nist
+ Jama
+ 1.0.2
+
+
+ net.sf.jgrapht
+ jgrapht
+ 0.8.3
+
+
+ org.freemarker
+ freemarker
+ 2.3.18
+
+
+ org.apache.commons
+ commons-email
+ 1.2
+
+
+ org.apache.commons
+ commons-jexl
+ 2.1.1
+
+
+ commons-lang
+ commons-lang
+ 2.5
+
+
+ commons-logging
+ commons-logging
+ 1.1.1
+
+
+ commons-io
+ commons-io
+ 2.1
+
+
+ commons-collections
+ commons-collections
+ 3.2.1
+
+
+ org.apache.commons
+ commons-math
+ 2.2
+
+
+ net.java.dev.jna
+ jna
+ 3.2.7
+
+
+ net.java.dev.jets3t
+ jets3t
+ 0.8.1
+
+
+ net.sf.gridscheduler
+ drmaa
+ 6.2u5p2
+
+
+ org.uncommons
+ reportng
+ 1.1.2
+
+
+ com.google.inject
+ guice
+ 3.0
+
+
+ org.apache.poi
+ poi
+ 3.8-beta3
+
+
+ org.apache.poi
+ poi-ooxml
+ 3.8-beta3
+
+
+ net.sf.snpeff
+ snpeff
+ 2.0.5
+
+
+ org.mongodb
+ mongo-java-driver
+ 2.7.3
+
+
+ com.google.code.gson
+ gson
+ 2.2.2
+
+
+ org.apache.httpcomponents
+ httpclient
+ 4.1.1
+
+
+
+
+ com.sun
+ tools
+ 1.4.2
+ system
+ ${java.home}/../lib/tools.jar
+
+
+
+ org.testng
+ testng
+ 6.8
+ test
+
+
+ com.google.caliper
+ caliper
+ 0.5-rc1
+ test
+
+
+
+ com.google.guava
+ guava
+
+
+
+
+
+
+
+
+
+
+
+ org.codehaus.mojo
+ exec-maven-plugin
+ 1.2.1
+
+
+ com.lukegb.mojo
+ gitdescribe-maven-plugin
+ 2.0
+
+
+ org.codehaus.mojo
+ build-helper-maven-plugin
+ 1.8
+
+
+ org.apache.maven.plugins
+ maven-clean-plugin
+ 2.5
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+ 2.8
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+ 2.6
+
+
+ org.apache.maven.plugins
+ maven-javadoc-plugin
+ 2.9.1
+
+
+ org.apache.maven.plugins
+ maven-compiler-plugin
+ 3.1
+
+
+ org.scala-tools
+ maven-scala-plugin
+ 2.15.2
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+ 2.4
+
+
+ org.apache.maven.plugins
+ maven-shade-plugin
+ 2.1
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+ 2.4
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-surefire-plugin
+ 2.16
+
+
+ true
+ false
+ false
+ plain
+ ${test.args}
+
+
+ usedefaultlisteners
+ false
+
+
+
+
+ diff
+ true
+
+ ${sting.pipelinetests.run}
+ ${java.io.tmpdir}
+
+
+
+
+ default-test
+ none
+
+
+
+ unit-tests
+
+ test
+
+
+
+ ${sting.unittests.skipped}
+
+ **/*Test.class
+
+
+ **/*IntegrationTest.class
+ **/*PipelineTest.class
+ **/*LargeScaleTest.class
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-failsafe-plugin
+ 2.16
+
+
+ true
+ false
+ false
+ plain
+ ${test.args}
+
+
+ usedefaultlisteners
+ false
+
+
+
+
+ diff
+ true
+
+ ${sting.pipelinetests.run}
+ ${java.io.tmpdir}
+
+
+
+
+ integration-tests
+
+ integration-test
+ verify
+
+
+
+
+ ${sting.integrationtests.skipped}
+
+ **/*IntegrationTest.class
+
+
+
+
+ pipeline-tests
+
+ integration-test
+ verify
+
+
+
+
+ ${sting.pipelinetests.skipped}
+
+ **/*PipelineTest.class
+
+
+
+
+ large-scale-tests
+
+ integration-test
+ verify
+
+
+
+ ${sting.largescaletests.skipped}
+
+ **/*LargeScaleTest.class
+
+
+
+
+
+
+
+ com.google.code.sortpom
+ maven-sortpom-plugin
+ 2.2
+
+ false
+ custom_1
+ \n
+ ${sourceEncoding}
+ true
+ scope
+ 4
+ false
+
+
+
+
+ sort
+
+ verify
+
+
+
+
+
+
+ com.pyx4j
+ maven-junction-plugin
+ 1.0.3
+
+
+ org.apache.maven.plugins
+ maven-invoker-plugin
+ 1.8
+
+
+ org.apache.maven.plugins
+ maven-install-plugin
+ 2.5
+
+
+ org.apache.maven.plugins
+ maven-site-plugin
+ 3.3
+
+
+
+
+
+
+
+ com.lukegb.mojo
+ gitdescribe-maven-plugin
+
+
+ --long
+
+ true
+ git.version
+
+
+
+ gitdescribe-initialize
+
+ gitdescribe
+
+ initialize
+
+
+ gitdescribe-presite
+
+ gitdescribe
+
+ pre-site
+
+
+
+
+ org.codehaus.mojo
+ build-helper-maven-plugin
+
+
+
+ fix-version-initialize
+
+ regex-property
+
+ initialize
+
+ build.version
+ ${git.version}
+ git-
+
+
+
+ fix-version-pre-site
+
+ regex-property
+
+ pre-site
+
+ build.version
+ ${git.version}
+ git-
+
+
+
+
+
+ com.google.code.sortpom
+ maven-sortpom-plugin
+
+
+ default
+
+ sort
+
+ verify
+
+
+
+
+
+
+
+ true
+
+
+
+
+ sting.public.repo.local
+ Sting Public Local Repository
+ file:${sting.basedir}/public/repo
+
+
+ sting.private.repo.local
+ Sting Private Local Repository
+ file:${sting.basedir}/private/repo
+
+
+
+
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
new file mode 100644
index 000000000..7e68cf740
--- /dev/null
+++ b/public/sting-utils/pom.xml
@@ -0,0 +1,170 @@
+
+
+ 4.0.0
+
+
+ org.broadinstitute.sting
+ sting-aggregator
+ 2.6-SNAPSHOT
+ ../..
+
+
+ sting-utils
+ jar
+ Sting Utils
+
+
+ ${project.basedir}/../..
+ org/broadinstitute/sting/utils/R
+ gsalib.tar.gz
+
+
+
+
+ net.sf
+ sam
+
+
+ net.sf
+ picard
+
+
+ org.broad
+ tribble
+
+
+ org.broadinstitute
+ variant
+
+
+ log4j
+ log4j
+
+
+ colt
+ colt
+
+
+ it.unimi.dsi
+ fastutil
+
+
+ org.simpleframework
+ simple-xml
+
+
+ org.reflections
+ reflections
+
+
+ org.slf4j
+ slf4j-log4j12
+
+
+ org.freemarker
+ freemarker
+
+
+ org.apache.commons
+ commons-jexl
+
+
+ commons-lang
+ commons-lang
+
+
+ commons-io
+ commons-io
+
+
+ commons-collections
+ commons-collections
+
+
+ org.apache.commons
+ commons-math
+
+
+ net.java.dev.jna
+ jna
+
+
+ net.java.dev.jets3t
+ jets3t
+
+
+ net.sf.gridscheduler
+ drmaa
+
+
+ com.google.code.gson
+ gson
+
+
+ org.apache.httpcomponents
+ httpclient
+
+
+ com.google.code.cofoja
+ cofoja
+
+
+ ${project.groupId}
+ gsalib
+ ${project.version}
+ tar.gz
+
+
+
+ org.testng
+ testng
+ test
+
+
+ com.google.caliper
+ caliper
+ test
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+ copy-gsalib
+
+ copy
+
+ process-resources
+
+
+
+ ${project.groupId}
+ gsalib
+ ${project.version}
+ tar.gz
+ ${project.build.outputDirectory}/${gsalib.packagedir}
+ ${gsalib.filename}
+
+
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+
+ test-jar
+
+
+
+
+
+
+