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‎README.txt‎

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SeqInCloud is a highly scalable parallel implementation of a popular
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genetic variant pipeline called genome analysis toolkit (GATK).
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SeqInCloud uses the Hadoop MapReduce framework and runs the
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workflow in a distributed fashion using multiple compute nodes
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provisioned either on-premises or in Microsoft Azure cloud.
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SeqInCloud is built on top of GATK version 1.6, which is freely
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available under a MIT License via the Broad Institute.
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This README contains instructions to build and run SeqInCloud.
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Building SeqInCloud
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===================
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1. Make sure that "java" and "ant" are installed and that the
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PATH environment is set correctly.
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2. Run "ant" from the directory containing the build.xml file
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in order to create the following two jar files in the "binaries"
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directory:
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a. SeqInCloud.jar, which is the main application jar file
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b. SICdeps.jar, which is the dependent jar file
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3. To rebuild, you can run "ant clean" followed by "ant"
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Running SeqInCloud
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==================
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1. Conigure a Hadoop cluster
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2. Load the dataset and the dependent jar (SICdeps.jar) into HDFS
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3. Run SeqInCloud with the command below. This provides a list of
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command-line options to use:
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# hadoop jar SeqInCloud.jar
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NOTE
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====
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The alignment stage in the pipeline is NOT optimized to use memory efficiently.
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The subsequent stages of the pipeline run fine, and hence, it is recommended to
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run SeqInCloud on an aligned BAM file.

‎build.xml‎

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‎ivy.xml‎

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<!--
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~ Copyright (c) 2012, The Broad Institute
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~
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<ivy-module version="1.0">
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<info organisation="org.broadinstitute" module="Sting"/>
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<configurations defaultconfmapping="test->default">
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<conf name="default" description="the core dependencies for the GATK"/>
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<conf name="test" extends="default" description="external dependencies used for testing and metrics" />
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<conf name="scala" extends="default" description="the dependencies for scala"/>
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<conf name="queue" extends="scala" description="the dependencies for Queue"/>
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</configurations>
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<dependencies defaultconf="default">
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<dependency org="net.sf" name="sam" rev="latest.integration"/>
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<dependency org="net.sf" name="picard" rev="latest.integration"/>
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<dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
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<!-- Tribble -->
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<dependency org="org.broad" name="tribble" rev="latest.integration"/>
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<dependency org="log4j" name="log4j" rev="1.2.15"/>
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<dependency org="javax.mail" name="mail" rev="1.4.4"/>
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<dependency org="colt" name="colt" rev="1.2.0"/>
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<!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
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<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
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<dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
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<!-- Dependencies for reflections mvn repository -->
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<dependency org="org.reflections" name="reflections" rev="0.9.7"/>
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<!-- Matrix package from math.nist.gov -->
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<dependency org="gov.nist" name="Jama" rev="1.0.2"/>
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<!-- Dependencies for the graph aligner -->
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<dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3"/>
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<!-- Dependencies for the html walker documention -->
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<dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>
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<!-- Commons Dependencies -->
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<dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
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<dependency org="org.apache.commons" name="commons-jexl" rev="2.0"/>
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<dependency org="commons-lang" name="commons-lang" rev="2.5"/>
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<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
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<dependency org="commons-io" name="commons-io" rev="2.1"/>
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<dependency org="commons-cli" name="commons-cli" rev="1.2"/>
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<dependency org="org.apache.commons" name="commons-math" rev="2.2" />
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<dependency org="com.google.collections" name="google-collections"
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rev="1.0"/>
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<dependency org="org.apache.hadoop" name="hadoop-core" rev="1.1.0" />
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<!-- Lucene core utilities -->
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<!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->
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<!-- Dependencies for LSF, DRMAA, and other C libraries -->
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<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
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<!-- Dependencies for amazon.com S3 support -->
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<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>
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<!-- Dependencies for GridEngine -->
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<dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
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<!-- Scala dependancies -->
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<dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
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<dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>
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<!-- testing and evaluation dependencies -->
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<dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
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<dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="test"/>
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<dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="test"/>
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<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="test"/>
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<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
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<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
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<!-- Contracts for Java and dependencies -->
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<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
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<dependency org="asm" name="asm-all" rev="3.3.1" />
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<!-- POI, for reading pipeline files -->
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<dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
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<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
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<!-- snpEff annotator for pipelines -->
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<dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5" />
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<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
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<exclude org="javax.servlet" />
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<exclude org="javax.jms" />
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<exclude org="com.sun.*" />
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</dependencies>
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</ivy-module>

‎licensing/Apache2.0_License.txt‎

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‎licensing/GATK1_LICENSE.txt‎

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Copyright (c) 2012 The Broad Institute
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Permission is hereby granted, free of charge, to any person
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obtaining a copy of this software and associated documentation
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files (the "Software"), to deal in the Software without
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restriction, including without limitation the rights to use,
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copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following
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conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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