HPC – Lampredi – software update – GATK & GATKQUEUE 2.7.2

Oct 022013

GATK 2.7.2 and GATKQUEUE 2.7.2 have been added to lampredi2. Details are:

$module load apps/gatk/2.7.2/noarch apps/gatk/2.7.2/noarch | OK

$ ls $GATKDIR bin GenomeAnalysisTK.jar resources

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$ module whatis apps/gatk/2.7.2/noarch apps/gatk/2.7.2 :


            Title: Genome Analysis Toolkit

          Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data

          License: Free for non-commercial use; registration required; see http://j.mp/TTba2N

            Group: Bioinformatics

              URL: http://www.broadinstitute.org/gatk/index.php
             Name: gatk

          Version: 2.7.2

           Module: apps/gatk/2.7.2/noarch

      Module path: /opt/gridware/etc/modules/apps/gatk/2.7.2/noarch

     Package path: /opt/gridware/pkg/apps/gatk/2.7.2/noarch
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: ext/gatk/2.7.2@9df24753

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T15:50:24

 Build parameters: tarball=/opt/gridware/ext/GenomeAnalysisTK-2.7-2.tar.bz2

         Compiler: N/A
For further information, execute:

module help apps/gatk/2.7.2/noarch

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$ module help apps/gatk/2.7.2/noarch


----------- Module Specific Help for 'apps/gatk/2.7.2/noarch' ---------------------------
              ======== Genome Analysis Toolkit ========

        Software package developed at the Broad Institute to

              analyse next-generation resequencing data

              ========================================              
This module sets up your environment for the use of the 'gatk'

application. This module sets up version '2.7.2' of the

application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

Please refer to the website for further details on usage of this package.
———————————————————————————-

$ module show apps/gatk/2.7.2/noarch ------------------------------------------------------------------- /opt/gridware/etc/modules/apps/gatk/2.7.2/noarch:


module-whatis	 
            Title: Genome Analysis Toolkit

          Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data

          License: Free for non-commercial use; registration required; see http://j.mp/TTba2N

            Group: Bioinformatics

              URL: http://www.broadinstitute.org/gatk/index.php
             Name: gatk

          Version: 2.7.2

           Module: apps/gatk/2.7.2/noarch

      Module path: /opt/gridware/etc/modules/apps/gatk/2.7.2/noarch

     Package path: /opt/gridware/pkg/apps/gatk/2.7.2/noarch
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: ext/gatk/2.7.2@9df24753

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T15:50:24

 Build parameters: tarball=/opt/gridware/ext/GenomeAnalysisTK-2.7-2.tar.bz2

         Compiler: N/A
For further information, execute:
	module help apps/gatk/2.7.2/noarch

module-conflict apps/gatk module-conflict apps/gatklite setenv GATKDIR /opt/gridware/pkg/apps/gatk/2.7.2/noarch setenv GATKBIN /opt/gridware/pkg/apps/gatk/2.7.2/noarch/bin setenv GATK_JAVA_MEM_MX 2g setenv GATK_JAVA_TMPDIR /tmp setenv GATK_JAVA_OPTS -Xmx$GATK_JAVA_MEM_MX -Djava.io.tmpdir=$GATK_JAVA_TMPDIR prepend-path PATH /opt/gridware/pkg/apps/gatk/2.7.2/noarch/bin
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GATKQUEUE 2.7.2

$ module load apps/gatkqueue/2.7.2/noarch apps/gatkqueue/2.7.2/noarch | -- apps/gatk/2.7.2/noarch | * --> OK | OK

$ ls $GATKQUEUEDIR bin java Queue.jar resources

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$ module whatis apps/gatkqueue/2.7.2/noarch apps/gatkqueue/2.7.2/noarch:


            Title: Genome Analysis Toolkit Queue

          Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines

          License: Free for non-commercial use; registration required; see http://j.mp/TTba2N

            Group: Bioinformatics

              URL: http://www.broadinstitute.org/gatk/index.php
             Name: gatkqueue

          Version: 2.7.2

           Module: apps/gatkqueue/2.7.2/noarch

      Module path: /opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch

     Package path: /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: ext/gatkqueue/2.7.2@95ff256d

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T15:50:50

 Build parameters: tarball=/opt/gridware/ext/Queue-2.7-2.tar.bz2

         Compiler: N/A

     Dependencies: apps/gatk/2.7.2/noarch (using: apps/gatk/2.7.2/noarch)
For further information, execute:

module help apps/gatkqueue/2.7.2/noarch

———————————————————————————-

$ module help apps/gatkqueue/2.7.2/noarch


----------- Module Specific Help for 'apps/gatkqueue/2.7.2/noarch' ---------------------------
           ======== Genome Analysis Toolkit Queue ========

     Command-line scripting framework for defining multi-stage

                     genomic analysis pipelines

           ==============================================           
This module sets up your environment for the use of the 'gatkqueue'

application. This module sets up version '2.7.2' of the

application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

Please refer to the website for further details on usage of this package.
———————————————————————————-

$ module show apps/gatkqueue/2.7.2/noarch ------------------------------------------------------------------- /opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch:


module-whatis	 
            Title: Genome Analysis Toolkit Queue

          Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines

          License: Free for non-commercial use; registration required; see http://j.mp/TTba2N

            Group: Bioinformatics

              URL: http://www.broadinstitute.org/gatk/index.php
             Name: gatkqueue

          Version: 2.7.2

           Module: apps/gatkqueue/2.7.2/noarch

      Module path: /opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch

     Package path: /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: ext/gatkqueue/2.7.2@95ff256d

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T15:50:50

 Build parameters: tarball=/opt/gridware/ext/Queue-2.7-2.tar.bz2

         Compiler: N/A

     Dependencies: apps/gatk/2.7.2/noarch (using: apps/gatk/2.7.2/noarch)
For further information, execute:
	module help apps/gatkqueue/2.7.2/noarch

module-prereq apps/gatk/2.7.2/noarch module-conflict apps/gatkqueue setenv GATKQUEUEDIR /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch setenv GATKQUEUEEXAMPLES /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/resources setenv GATKQUEUEBIN /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/bin setenv GATKQUEUE_JAVA_MEM_MX 2g setenv GATKQUEUE_JAVA_TMPDIR /tmp setenv GATKQUEUE_JAVA_OPTS -Xmx$GATKQUEUE_JAVA_MEM_MX -Djava.io.tmpdir=$GATKQUEUE_JAVA_TMPDIR prepend-path PATH /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/bin
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Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
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