This page was last updated on Wednesday, 25-Apr-2018 12:22:14 CDT

Installation notes for the GATK 2 version 2.5-2

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Prerequisites

java

Installation V.4.x

1. Create an account on gatk web site http://www.broadinstitute.org/gatk/index.php
2. Download manually to /programinstallers
3. $ ver="4.0.3.0"
4. $ cd /usr/local/bin/
5. $ unzip /programinstallers/gatk-$ver.zip
6. Make a version-independent symlink
   $ ln -s gatk-$ver GenomeAnalysisTK
7. Add to default PATH
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/GenomeAnalysisTK"
   …

Installation V.3.x

1. Create an account on gatk web site http://www.broadinstitute.org/gatk/index.php
2. Download manually to /programinstallers
3. $ ver="2.5-2"; hex="gf57256b"
   Or if installing the nightly build, file name looks like GenomeAnalysisTK-nightly-2014-04-14-g744780d.tar.bz2
   Get the file name from https://www.broadinstitute.org/gatk/nightly
   $ ver="nightly-2014-04-14"; hex="-g744780d"
4. $ cd /usr/local/bin/
5. Warning - version 3.1-1 is a tar bomb. Add this step:
   $ mkdir GenomeAnalysisTK-$ver && cd GenomeAnalysisTK-$ver
6. $ tar -jxvf /programinstallers/GenomeAnalysisTK-$ver$hex.tar.bz2
   

   GenomeAnalysisTK-2.5-2-gf57256b/
   GenomeAnalysisTK-2.5-2-gf57256b/resources/
   GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar
   GenomeAnalysisTK-2.5-2-gf57256b/resources/CheckPileup.java
   GenomeAnalysisTK-2.5-2-gf57256b/resources/CountLoci.java
   GenomeAnalysisTK-2.5-2-gf57256b/resources/CountReads.java
   GenomeAnalysisTK-2.5-2-gf57256b/resources/Pileup.java
   GenomeAnalysisTK-2.5-2-gf57256b/resources/PrintReads.java
   GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleBAM.bam
   GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleBAM.bam.bai
   GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.dict
   GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.fasta
   GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.fasta.fai

7. $ cd ..
8. Make a version-independent symlink
   $ ln -s GenomeAnalysisTK-$ver$hex GenomeAnalysisTK
9. Test as described at http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
   $ java -jar GenomeAnalysisTK/GenomeAnalysisTK.jar --help
10. Make a wrapper for convenience

    #!/bin/bash
    # memory for Java in gigabytes
    defaultjmem=4
    jmem=$defaultjmem
    if [[ $1 =~ ^[0-9]+$ ]] ; then
      jmem=$1
      shift
      echo "Will allocate $jmem gigabytes of memory for GATK"
    fi
    if [[ "$1" == "" ]]; then
      echo "This is a Java wrapper for GATK"
      echo "Pass in the required parameters"
      echo "e.g. gatk -T LiftoverVariants ..."
      echo "Default memory allocation is $defaultjmem gigabytes"
      echo "To specify an alternate amount, e.g. 16 gigabytes, pass in \"16\" before any other parameters"
      echo "e.g. gatk 16 -T LiftoverVariants ..."
      exit 1
    else
      java -Xmx${jmem}g -jar /usr/local/bin/GenomeAnalysisTK/GenomeAnalysisTK.jar "$@"
      r=$?; if [ $r != 0 ]; then echo "Picard returned error code $r"; fi
      exit $r
    fi

11. $ chmod +x gatk