HPC – Lampredi – software update – GATK and GATK Queue 3.1.1

 Uncategorized  No Responses »
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
x8625

HPC – Lampredi – software update – Annovar 529 (2012-09-20)

 Uncategorized  No Responses »
Apr 112014
  
$ module load apps/annovar/529
apps/annovar/529/noarch
 |
 OK

$ ls $ANNOVARBIN
annotate_variation.pl  coding_change.pl 
convert2annovar.pl  retrieve_seq_from_fasta.pl
summarize_annovar.pl  table_annovar.pl 
variants_reduction.pl

$ ls $ANNOVARDIR
bin  db  example

$ module whatis apps/annovar/529/noarch

 apps/annovar/529 :

Title: ANNOVAR
 Summary: Functional annotation of genetic variants from high-throughput sequencing data
 License: NONFREE - Free for non-profit use; see http://www.openbioinformatics.org/annovar/annovar_faq.html#license
 Group: Bioinformatics
 URL: http://www.openbioinformatics.org/annovar/

Name: annovar
 Version: 529
 Module: apps/annovar/529/noarch
 Module path: /opt/gridware/etc/modules/apps/annovar/529/noarch
 Package path: /opt/gridware/pkg/apps/annovar/529/noarch

Repository: git+http://download.alces-software.com/git/packager-base@c0cb517
 Package: ext/annovar/@094f23e0
 Last update: 2012-09-20

Builder: root@headnode1.lampredi.cluster.local
 Build date: 2014-04-11T13:12:32
 Build parameters: tarball=/opt/gridware/ext/annovar-20130823.tar.gz
 Compiler: N/A

For further information, execute:
module help apps/annovar/529/noarch

$ module help apps/annovar/529/noarch

----------- Module Specific Help for 'apps/annovar/529/noarch' ---------------------------


                      ======== ANNOVAR ========                      
           Functional annotation of genetic variants from            
                   high-throughput sequencing data                   
                      ========================                      

This module sets up your environment for the use of the 'annovar'
application. This module sets up version '529' of the
application.


>> SYNOPSIS <1%) in the
    1000 Genome Project, or identify subset of non-synonymous SNPs
    with SIFT score>0.05, or many other annotations on specific
    mutations.
  * Other functionalities: Retrieve the nucleotide sequence in any
    user-specific genomic positions in batch, identify a candidate
    gene list for Mendelian diseases from exome data, identify a
    list of SNPs from 1000 Genomes that are in strong LD with a GWAS
    hit, and many other creative utilities.


>> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

$ module show apps/annovar/529/noarch

-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/annovar/529/noarch:

module-whatis	 

            Title: ANNOVAR
          Summary: Functional annotation of genetic variants from high-throughput sequencing data
          License: NONFREE - Free for non-profit use; see http://www.openbioinformatics.org/annovar/annovar_faq.html#license
            Group: Bioinformatics
              URL: http://www.openbioinformatics.org/annovar/

             Name: annovar
          Version: 529
           Module: apps/annovar/529/noarch
      Module path: /opt/gridware/etc/modules/apps/annovar/529/noarch
     Package path: /opt/gridware/pkg/apps/annovar/529/noarch

       Repository: git+http://download.alces-software.com/git/packager-base@c0cb517
          Package: ext/annovar/@094f23e0
      Last update: 2012-09-20

          Builder: root@headnode1.lampredi.cluster.local
       Build date: 2014-04-11T13:12:32
 Build parameters: tarball=/opt/gridware/ext/annovar-20130823.tar.gz
         Compiler: N/A


For further information, execute:

	module help apps/annovar/529/noarch
 
module-conflict	 apps/annovar 
setenv		 ANNOVARDIR /opt/gridware/pkg/apps/annovar/529/noarch 
setenv		 ANNOVARBIN /opt/gridware/pkg/apps/annovar/529/noarch/bin 
prepend-path	 PATH /opt/gridware/pkg/apps/annovar/529/noarch/bin 
prepend-path	 MANPATH /opt/gridware/pkg/apps/annovar/529/noarch/share/man 
-------------------------------------------------------------------

Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
x8625

 Posted by at 2:42 pm