diff --git a/BiopetRoot.iml b/BiopetRoot.iml new file mode 100644 index 0000000000000000000000000000000000000000..65b49ee12b35fb025f2ff7dee4698415bdc360e3 --- /dev/null +++ b/BiopetRoot.iml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file diff --git a/protected/BiopetGatk.iml b/protected/BiopetGatk.iml new file mode 100644 index 0000000000000000000000000000000000000000..65b49ee12b35fb025f2ff7dee4698415bdc360e3 --- /dev/null +++ b/protected/BiopetGatk.iml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file diff --git a/protected/basty/Basty.iml b/protected/basty/Basty.iml new file mode 100644 index 0000000000000000000000000000000000000000..fb9121d5fa34a78471f7453cbf17fae04ab8a3e3 --- /dev/null +++ b/protected/basty/Basty.iml @@ -0,0 +1,97 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="BiopetGatkPipelines" /> + <orderEntry type="module" module-name="BiopetGatkExtensions" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file diff --git a/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml b/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml new file mode 100644 index 0000000000000000000000000000000000000000..93f504d0422488b4a3c8dba634ced25e639c678b --- /dev/null +++ b/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml @@ -0,0 +1,92 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + </component> +</module> \ No newline at end of file diff --git a/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml b/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml new file mode 100644 index 0000000000000000000000000000000000000000..326e841ffaa063db06bb7de76a633504ef5f79f2 --- /dev/null +++ b/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml @@ -0,0 +1,96 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="BiopetGatkExtensions" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file diff --git a/protected/biopet-protected-package/BiopetProtectedPackage.iml b/protected/biopet-protected-package/BiopetProtectedPackage.iml new file mode 100644 index 0000000000000000000000000000000000000000..27fc34a1f8346680c9ba37b1b675eae8e1a21366 --- /dev/null +++ b/protected/biopet-protected-package/BiopetProtectedPackage.iml @@ -0,0 +1,102 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="BiopetPublicPackage" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="BamMetrics" /> + <orderEntry type="module" module-name="Gentrap" /> + <orderEntry type="module" module-name="Sage" /> + <orderEntry type="module" module-name="Yamsvp" /> + <orderEntry type="module" module-name="BiopetGatkPipelines" /> + <orderEntry type="module" module-name="BiopetGatkExtensions" /> + <orderEntry type="module" module-name="Basty" /> + </component> +</module> \ No newline at end of file diff --git a/public/Biopet.iml b/public/Biopet.iml new file mode 100644 index 0000000000000000000000000000000000000000..9120ea623670da6fa98d7f004662ab238a4fa936 --- /dev/null +++ b/public/Biopet.iml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file diff --git a/public/bammetrics/BamMetrics.iml b/public/bammetrics/BamMetrics.iml new file mode 100644 index 0000000000000000000000000000000000000000..dc0afbee2ccf2f185458a930863b52ade6962739 --- /dev/null +++ b/public/bammetrics/BamMetrics.iml @@ -0,0 +1,92 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + </component> +</module> \ No newline at end of file diff --git a/public/biopet-framework/BiopetFramework.iml b/public/biopet-framework/BiopetFramework.iml new file mode 100644 index 0000000000000000000000000000000000000000..e322ea86900799ffc7e4257ea45cebede0c633a5 --- /dev/null +++ b/public/biopet-framework/BiopetFramework.iml @@ -0,0 +1,101 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" /> + <orderEntry type="library" name="Maven: junit:junit:4.10" level="project" /> + <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" /> + <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" /> + <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" /> + <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" /> + <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" /> + <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + </component> +</module> \ No newline at end of file diff --git a/public/biopet-public-package/BiopetPublicPackage.iml b/public/biopet-public-package/BiopetPublicPackage.iml new file mode 100644 index 0000000000000000000000000000000000000000..384a22df7bc2df4a29e9b5b0e7eed0a8c6a219c9 --- /dev/null +++ b/public/biopet-public-package/BiopetPublicPackage.iml @@ -0,0 +1,98 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="BamMetrics" /> + <orderEntry type="module" module-name="Gentrap" /> + <orderEntry type="module" module-name="Sage" /> + <orderEntry type="module" module-name="Yamsvp" /> + </component> +</module> \ No newline at end of file diff --git a/public/flexiprep/Flexiprep.iml b/public/flexiprep/Flexiprep.iml new file mode 100644 index 0000000000000000000000000000000000000000..dc0afbee2ccf2f185458a930863b52ade6962739 --- /dev/null +++ b/public/flexiprep/Flexiprep.iml @@ -0,0 +1,92 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + </component> +</module> \ No newline at end of file diff --git a/public/gentrap/Gentrap.iml b/public/gentrap/Gentrap.iml new file mode 100644 index 0000000000000000000000000000000000000000..e1eb4b5603b6bdbe4340c36aa195798b205535db --- /dev/null +++ b/public/gentrap/Gentrap.iml @@ -0,0 +1,95 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file diff --git a/public/mapping/Mapping.iml b/public/mapping/Mapping.iml new file mode 100644 index 0000000000000000000000000000000000000000..c76cc7f3bf70d48923f895e158c35dbd72b6af78 --- /dev/null +++ b/public/mapping/Mapping.iml @@ -0,0 +1,94 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file diff --git a/public/sage/Sage.iml b/public/sage/Sage.iml new file mode 100644 index 0000000000000000000000000000000000000000..e1eb4b5603b6bdbe4340c36aa195798b205535db --- /dev/null +++ b/public/sage/Sage.iml @@ -0,0 +1,95 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file diff --git a/public/toucan/Toucan.iml b/public/toucan/Toucan.iml new file mode 100644 index 0000000000000000000000000000000000000000..dc0afbee2ccf2f185458a930863b52ade6962739 --- /dev/null +++ b/public/toucan/Toucan.iml @@ -0,0 +1,92 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + </component> +</module> \ No newline at end of file diff --git a/public/yamsvp/Yamsvp.iml b/public/yamsvp/Yamsvp.iml new file mode 100644 index 0000000000000000000000000000000000000000..e1eb4b5603b6bdbe4340c36aa195798b205535db --- /dev/null +++ b/public/yamsvp/Yamsvp.iml @@ -0,0 +1,95 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="false"> + <output url="file://$MODULE_DIR$/target/classes" /> + <output-test url="file://$MODULE_DIR$/target/test-classes" /> + <content url="file://$MODULE_DIR$"> + <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" /> + <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> + <excludeFolder url="file://$MODULE_DIR$/target" /> + </content> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + <orderEntry type="module" module-name="BiopetFramework" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" /> + <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" /> + <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" /> + <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" /> + <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools:1.4.2"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" /> + <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" /> + <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" /> + <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" /> + <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" /> + <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" /> + <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" /> + <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" /> + <orderEntry type="module-library"> + <library name="Maven: com.sun:tools.jar:1.5"> + <CLASSES> + <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" /> + </CLASSES> + <JAVADOC /> + <SOURCES /> + </library> + </orderEntry> + <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" /> + <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" /> + <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" /> + <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" /> + <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" /> + <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" /> + <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" /> + <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" /> + <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" /> + <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" /> + <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" /> + <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" /> + <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" /> + <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" /> + <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" /> + <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" /> + <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" /> + <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" /> + <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" /> + <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" /> + <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" /> + <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" /> + <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" /> + <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> + <orderEntry type="module" module-name="Mapping" /> + <orderEntry type="module" module-name="Flexiprep" /> + <orderEntry type="module" module-name="BamMetrics" /> + </component> +</module> \ No newline at end of file