Apr 142014
$ module load apps/gatk/3.1.1/noarch apps/gatk/3.1.1/noarch | OK $ ls $GATKDIR bin GenomeAnalysisTK.jar Queue.jar resources $ ls $GATKBIN gatk gatk_ErrorThrowing gatk_ReadBackedPhasing gatk_AnalyzeCovariates gatk_FastaAlternateReferenceMaker gatk_ReadClippingStats gatk_ApplyRecalibration gatk_FastaReferenceMaker gatk_ReadGroupProperties gatk_BaseCoverageDistribution gatk_FastaStats gatk_ReadLengthDistribution gatk_BaseRecalibrator gatk_FilterLiftedVariants gatk_RealignerTargetCreator gatk_BeagleOutputToVCF gatk_FindCoveredIntervals gatk_RegenotypeVariants gatk_CalculateGenotypePosteriors gatk_FlagStat gatk_SelectHeaders gatk_CallableLoci gatk_GATKPaperGenotyper gatk_SelectVariants gatk_CheckAlignment gatk_GCContentByInterval gatk_SimulateReadsForVariants gatk_CheckPileup gatk_GenotypeAndValidate gatk_SplitNCigarReads gatk_ClipReads gatk_GenotypeConcordance gatk_SplitSamFile gatk_CombineGVCFs gatk_GenotypeGVCFs gatk_UnifiedGenotyper gatk_CombineVariants gatk_HaplotypeCaller gatk_ValidateVariants gatk_CompareCallableLoci gatk_HaplotypeResolver gatk_ValidationAmplicons gatk_CountBases gatk_IndelRealigner gatk_ValidationSiteSelector gatk_CountIntervals gatk_LeftAlignAndTrimVariants gatk_VariantAnnotator gatk_CountLoci gatk_LeftAlignIndels gatk_VariantEval gatk_CountMales gatk_LiftoverVariants gatk_VariantFiltration gatk_CountReadEvents gatk_PhaseByTransmission gatk_VariantRecalibrator gatk_CountReads gatk_Pileup gatk_VariantsToAllelicPrimitives gatk_CountRODs gatk_PrintReads gatk_VariantsToBeagleUnphased gatk_CountRODsByRef gatk_PrintRODs gatk_VariantsToBinaryPed gatk_CountTerminusEvent gatk_ProduceBeagleInput gatk_VariantsToTable gatk_CoveredByNSamplesSites gatk_QCRef gatk_VariantsToVCF gatk_DepthOfCoverage gatk_QualifyMissingIntervals gatk_VariantValidationAssessor gatk_DiagnoseTargets gatk-queue GenomeAnalysisTK gatk_DiffObjects gatk_RandomlySplitVariants Queue gatk_ErrorRatePerCycle gatk_ReadAdaptorTrimmer
$ module show apps/gatk/3.1.1/noarch
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/gatk/3.1.1/noarch:
module-whatis
Title: Genome Analysis Toolkit + Queue
Summary: Broad Institute package for analysing next-generation resequencing data; including 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: gatk
Version: 3.1.1
Module: apps/gatk/3.1.1/noarch
Module path: /opt/gridware/etc/modules/apps/gatk/3.1.1/noarch
Package path: /opt/gridware/pkg/apps/gatk/3.1.1/noarch
Repository: file:/opt/gridware/etc/repos/local
Package: ext/gatk+queue/3.x@05599477
Last update: 2014-04-14
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-04-14T10:58:33
Build parameters: gatktarball=/opt/gridware/ext/GenomeAnalysisTK-3.1-1.tar.bz2 gatkqueuetarball=/opt/gridware/ext/Queue-3.1-1.tar.bz2 tarversion=3.1.1
Compiler: N/A
For further information, execute:
module help apps/gatk/3.1.1/noarch
module-conflict apps/gatk
module-conflict apps/gatklite
setenv GATKDIR /opt/gridware/pkg/apps/gatk+queue/3.1.1/noarch
setenv GATKBIN /opt/gridware/pkg/apps/gatk+queue/3.1.1/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+queue/3.1.1/noarch/bin
-------------------------------------------------------------------
$ whatis apps/gatk/3.1.1/noarch
apps/gatk/3.1.1/noarch: nothing appropriate
[nas18@login1(lampredi) ~]$ module whatis apps/gatk/3.1.1/noarch
apps/gatk/3.1.1/noarch:
Title: Genome Analysis Toolkit + Queue
Summary: Broad Institute package for analysing next-generation resequencing data; including 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: gatk
Version: 3.1.1
Module: apps/gatk/3.1.1/noarch
Module path: /opt/gridware/etc/modules/apps/gatk/3.1.1/noarch
Package path: /opt/gridware/pkg/apps/gatk/3.1.1/noarch
Repository: file:/opt/gridware/etc/repos/local
Package: ext/gatk+queue/3.x@05599477
Last update: 2014-04-14
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-04-14T10:58:33
Build parameters: gatktarball=/opt/gridware/ext/GenomeAnalysisTK-3.1-1.tar.bz2 gatkqueuetarball=/opt/gridware/ext/Queue-3.1-1.tar.bz2 tarversion=3.1.1
Compiler: N/A
For further information, execute:
module help apps/gatk/3.1.1/noarch
$ module help apps/gatk/3.1.1/noarch
----------- Module Specific Help for 'apps/gatk/3.1.1/noarch' ---------------------------
======== Genome Analysis Toolkit + Queue ========
Broad Institute package for analysing next-generation
resequencing data; including command-line scripting
framework for defining multi-stage genomic analysis
pipelines
================================================
This module sets up your environment for the use of the 'gatk'
application. This module sets up version '3.1.1' of the
application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<
Please refer to the website for further details on usage of this
package.
$ module load apps/gatkqueue/3.1.1/noarch apps/gatkqueue/3.1.1/noarch | OK
$ module show apps/gatkqueue/3.1.1/noarch
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/gatkqueue/3.1.1/noarch:
module-whatis
Title: Genome Analysis Toolkit + Queue
Summary: Broad Institute package for analysing next-generation resequencing data; including 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: 3.1.1
Module: apps/gatkqueue/3.1.1/noarch
Module path: /opt/gridware/etc/modules/apps/gatkqueue/3.1.1/noarch
Package path: /opt/gridware/pkg/apps/gatkqueue/3.1.1/noarch
Repository: file:/opt/gridware/etc/repos/local
Package: ext/gatk+queue/3.x@05599477
Last update: 2014-04-14
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-04-14T10:58:34
Build parameters: gatktarball=/opt/gridware/ext/GenomeAnalysisTK-3.1-1.tar.bz2 gatkqueuetarball=/opt/gridware/ext/Queue-3.1-1.tar.bz2 tarversion=3.1.1
Compiler: N/A
For further information, execute:
module help apps/gatkqueue/3.1.1/noarch
module-conflict apps/gatkqueue
setenv GATKQUEUEDIR /opt/gridware/pkg/apps/gatk+queue/3.1.1/noarch
setenv GATKQUEUEEXAMPLES /opt/gridware/pkg/apps/gatk+queue/3.1.1/noarch/resources
setenv GATKQUEUEBIN /opt/gridware/pkg/apps/gatk+queue/3.1.1/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/gatk+queue/3.1.1/noarch/bin
-------------------------------------------------------------------
$ module whatis apps/gatkqueue/3.1.1/noarch
apps/gatkqueue/3.1.1/noarch:
Title: Genome Analysis Toolkit + Queue
Summary: Broad Institute package for analysing next-generation resequencing data; including 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: 3.1.1
Module: apps/gatkqueue/3.1.1/noarch
Module path: /opt/gridware/etc/modules/apps/gatkqueue/3.1.1/noarch
Package path: /opt/gridware/pkg/apps/gatkqueue/3.1.1/noarch
Repository: file:/opt/gridware/etc/repos/local
Package: ext/gatk+queue/3.x@05599477
Last update: 2014-04-14
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-04-14T10:58:34
Build parameters: gatktarball=/opt/gridware/ext/GenomeAnalysisTK-3.1-1.tar.bz2 gatkqueuetarball=/opt/gridware/ext/Queue-3.1-1.tar.bz2 tarversion=3.1.1
Compiler: N/A
For further information, execute:
module help apps/gatkqueue/3.1.1/noarch
$ module help apps/gatkqueue/3.1.1/noarch
----------- Module Specific Help for 'apps/gatkqueue/3.1.1/noarch' ---------------------------
======== Genome Analysis Toolkit + Queue ========
Broad Institute package for analysing next-generation
resequencing data; including 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 '3.1.1' of the
application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<
Please refer to the website for further details on usage of this
package.
Lampredi HPC
igm-lampredi-users@ncl.ac.uk
IGM IT
igmithelp@ncl.ac.uk
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