HPC – Lampredi – software update – Breakpointer 1.0

 Uncategorized  No Responses »
May 062014
  
$ module load apps/breakpointer/1.0/bin
 apps/breakpointer/1.0/bin
 | -- apps/bwa/0.6.2/gcc-4.4.6
 | | -- libs/gcc/system
 | | * --> OK
 | * --> OK
 | -- apps/samtools/0.1.8/gcc-4.4.6
 | | -- libs/gcc/system ... SKIPPED (already loaded)
 | * --> OK
 |
 OK
$ ls $BREAKPOINTERBIN
 BreakPointer BreakPointer.sh fh_BreakPointerScatter
$ ls $BREAKPOINTERDIR
 bin doc lib share
$ module whatis apps/breakpointer
apps/breakpointer    : 

            Title: BreakPointer
          Summary: Pinpoint rearrangement breakpoints using paired end reads
          License: NONFREE - For academic non-commercial research purposes only
            Group: Bioinformatics
              URL: http://www.broadinstitute.org/cancer/cga/breakpointer

             Name: breakpointer
          Version: 1.0
           Module: apps/breakpointer/1.0/bin
      Module path: /opt/gridware/etc/modules/apps/breakpointer/1.0/bin
     Package path: /opt/gridware/pkg/apps/breakpointer/1.0/bin

       Repository: git+http://download.alces-software.com/git/packager-base@cdc9148
          Package: ext/breakpointer/1.0@9068e192
      Last update: 2014-05-02

          Builder: root@headnode1.lampredi.cluster.local
       Build date: 2014-05-02T15:29:09
 Build parameters: tarball=/opt/gridware/ext/BreakPointer_1.0.tar
         Compiler: N/A
     Dependencies: apps/bwa/0.6.2/gcc-4.4.6 (using: apps/bwa/0.6.2/gcc-4.4.6)
                   apps/samtools/0.1.8/gcc-4.4.6 (using: apps/samtools/0.1.8/gcc-4.4.6)

For further information, execute:

	module help apps/breakpointer/1.0/bin

>> GET STARTED <<

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

$ module show apps/breakpointer/1.0/bin

/opt/gridware/etc/modules/apps/breakpointer/1.0/bin:

module-whatis	 

            Title: BreakPointer
          Summary: Pinpoint rearrangement breakpoints using paired end reads
          License: NONFREE - For academic non-commercial research purposes only
            Group: Bioinformatics
              URL: http://www.broadinstitute.org/cancer/cga/breakpointer

             Name: breakpointer
          Version: 1.0
           Module: apps/breakpointer/1.0/bin
      Module path: /opt/gridware/etc/modules/apps/breakpointer/1.0/bin
     Package path: /opt/gridware/pkg/apps/breakpointer/1.0/bin

       Repository: git+http://download.alces-software.com/git/packager-base@cdc9148
          Package: ext/breakpointer/1.0@9068e192
      Last update: 2014-05-02

          Builder: root@headnode1.lampredi.cluster.local
       Build date: 2014-05-02T15:29:09
 Build parameters: tarball=/opt/gridware/ext/BreakPointer_1.0.tar
         Compiler: N/A
     Dependencies: apps/bwa/0.6.2/gcc-4.4.6 (using: apps/bwa/0.6.2/gcc-4.4.6)
                   apps/samtools/0.1.8/gcc-4.4.6 (using: apps/samtools/0.1.8/gcc-4.4.6)

For further information, execute:

	module help apps/breakpointer/1.0/bin
 
module-prereq	 apps/bwa/0.6.2/gcc-4.4.6 
module-prereq	 apps/samtools/0.1.8/gcc-4.4.6 
module-conflict	 apps/breakpointer 
setenv		 BREAKPOINTERDIR /opt/gridware/pkg/apps/breakpointer/1.0/bin 
setenv		 BREAKPOINTERBIN /opt/gridware/pkg/apps/breakpointer/1.0/bin/bin 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/sys/java/jre/glnxa64/jre/lib/amd64 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/sys/java/jre/glnxa64/jre/lib/amd64/client 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/sys/java/jre/glnxa64/jre/lib/amd64/server 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/sys/java/jre/glnxa64/jre/lib/amd64/native_threads 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/sys/os/glnxa64 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/bin/glnxa64 
prepend-path	 LD_LIBRARY_PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/runtime/glnxa64 
setenv		 XAPPLRESDIR /opt/gridware/pkg/apps/breakpointer/1.0/bin/lib/mcr/v710/X11/app-defaults 
prepend-path	 PATH /opt/gridware/pkg/apps/breakpointer/1.0/bin/bin

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

IGM IT
igmithelp@ncl.ac.uk
x8625

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 – JAGS v3.4.0

 Uncategorized  No Responses »
Feb 282014
 

JAGS 3.4.0,  Just Another Gibbs Sampler.  It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation  not wholly unlike BUGS.

http://mcmc-jags.sourceforge.net/

 

---------------------------------------------------------------------------------

$ module load apps/jags

apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

| — libs/gcc/system

|    * –> OK

|

OK

$ ls $JAGSDIR

bin  include  lib  libexec  share

 

$ ls $JAGSBIN

jags

 

$ jags

Welcome to JAGS 3.4.0 on Fri Feb 28 13:13:48 2014

JAGS is free software and comes with ABSOLUTELY NO WARRANTY

Loading module: basemod: ok

Loading module: bugs: ok

 

---------------------------------------------------------------------------------

$ module whatis apps/jags

apps/jags            :

Title: JAGS

Summary: Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation

License: GPLv2

Group: Bioinformatics

URL: http://mcmc-jags.sourceforge.net/

 

Name: jags

Version: 3.4.0

Module: apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

Module path: /opt/gridware/etc/modules/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

Package path: /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

 

Repository: file:/opt/gridware/etc/repos/local

Package: apps/jags/3.4.0@08f607cc

Last update: 2014-02-28

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-28T11:48:10

Build modules: libs/atlas/3.10.0/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

 

For further information, execute:

 

module help apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

---------------------------------------------------------------------------------

$ module help apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

 

———– Module Specific Help for ‘apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0’ —————————

======== JAGS ========

Analysis of Bayesian hierarchical models using Markov Chain

Monte Carlo simulation

=====================

This module sets up your environment for the use of the ‘jags’

application. This module sets up version ‘3.4.0’ of the

application.

 

>> SYNOPSIS <<

JAGS is Just Another Gibbs Sampler.  It is a program for analysis of

Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)

simulation not wholly unlike BUGS.  JAGS was written with three aims

in mind:

* To have a cross-platform engine for the BUGS language.

* To be extensible, allowing users to write their own functions,

distributions and samplers.

* To be a plaftorm for experimentation with ideas in Bayesian

modelling.

 

>> LICENSING <<

This package is made available subject to the following license(s):

GPLv2

Please refer to the website for further details regarding licensing.

 

>> FURTHER INFORMATION <<

More information about this software can be found at the website:

http://mcmc-jags.sourceforge.net/

For further details regarding this module, including the environment

modifications it will apply, execute:

 

module show apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

>> GET STARTED <<

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

package.

---------------------------------------------------------------------------------

$ module show apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

——————————————————————-

/opt/gridware/etc/modules/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0:

module-whatis

Title: JAGS

Summary: Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation

License: GPLv2

Group: Bioinformatics

URL: http://mcmc-jags.sourceforge.net/

 

Name: jags

Version: 3.4.0

Module: apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

Module path: /opt/gridware/etc/modules/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

Package path: /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

 

Repository: file:/opt/gridware/etc/repos/local

Package: apps/jags/3.4.0@08f607cc

Last update: 2014-02-28

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-28T11:48:10

Build modules: libs/atlas/3.10.0/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

 

For further information, execute:

module help apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

module-prereq libs/gcc/system

module-conflict apps/jags

setenv JAGSDIR /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0

setenv JAGSBIN /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/bin

setenv JAGSLIB /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/lib

setenv JAGSINCLUDE /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/include

prepend-path LD_LIBRARY_PATH /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/lib

prepend-path MANPATH /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/share/man

prepend-path PKG_CONFIG_PATH /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/lib/pkgconfig

prepend-path PATH /opt/gridware/pkg/apps/jags/3.4.0/gcc-4.4.6+atlas-3.10.0/bin

———————————————————————————

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – MitoSeek 1.2

 Uncategorized  No Responses »
Feb 242014
 

MitoSeek has been updated to version 1.2, as of 24/02/2014

This is a software tool to reliably and easily extract mitochondrial genome information from exome sequencing data.

https://github.com/riverlee/MitoSeek

——————————————————————-

$ module load apps/mitoseek/1.2

apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

| — libs/gcc/system

|    * –> OK

| — apps/perl/5.16.1/gcc-4.4.6

|    | — libs/gcc/system … SKIPPED (already loaded)

|    * –> OK

| — apps/samtools/0.1.18/gcc-4.4.6

|    | — libs/gcc/system … SKIPPED (already loaded)

|    * –> OK

|

OK

 

——————————————————————-

 

$ module whatis apps/mitoseek/1.2

apps/mitoseek/1.2    :

 

Title: MitoSeek

Summary: Extraction of mitochondrial genome information from exome sequencing data

License: GPLv2

Group: Bioinformatics

URL: https://github.com/riverlee/MitoSeek

 

Name: mitoseek

Version: 1.2

Module: apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

Module path: /opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

Package path: /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

 

Repository: file:/opt/gridware/etc/repos/local

Package: apps/mitoseek/1.2@6ea5eade

Last update: 2014-02-24

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T11:08:18

Build modules: apps/perl/5.16.1/gcc-4.4.6, apps/samtools/0.1.18/gcc-4.4.6, apps/cpanminus/1.5017/noarch

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

apps/perl/5.16.1/gcc-4.4.6 (using: apps/perl/5.16.1/gcc-4.4.6)

apps/samtools/0.1.18/gcc-4.4.6 (using: apps/samtools/0.1.18/gcc-4.4.6)

 

For further information, execute:

 

module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

——————————————————————-

 

$ module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

 

———– Module Specific Help for ‘apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18’ —————————

 

 

======== MitoSeek ========

Extraction of mitochondrial genome information from exome

sequencing data

=========================

 

This module sets up your environment for the use of the ‘mitoseek’

application. This module sets up version ‘1.2’ of the

application.

 

 

>> SYNOPSIS <<

 

MitoSeek is an open-source software tool to reliably and easily

extract mitochondrial genome information from exome sequencing data.

MitoSeek evaluates mitochondrial genome alignment quality, estimates

relative mitochondrial copy numbers, and detects heteroplasmy,

somatic mutation, and structural variance of the mitochondrial

genome.

 

 

>> LICENSING <<

 

This package is made available subject to the following license(s):

 

GPLv2

 

Please refer to the website for further details regarding licensing.

 

 

>> FURTHER INFORMATION <<

 

More information about this software can be found at the website:

 

https://github.com/riverlee/MitoSeek

 

For further details regarding this module, including the environment

modifications it will apply, execute:

 

module show apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

 

 

>> GET STARTED <<

 

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

package.

——————————————————————-

 

$ module show apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

——————————————————————-

/opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18:

 

module-whatis

 

Title: MitoSeek

Summary: Extraction of mitochondrial genome information from exome sequencing data

License: GPLv2

Group: Bioinformatics

URL: https://github.com/riverlee/MitoSeek

 

Name: mitoseek

Version: 1.2

Module: apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

Module path: /opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

Package path: /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

 

Repository: file:/opt/gridware/etc/repos/local

Package: apps/mitoseek/1.2@6ea5eade

Last update: 2014-02-24

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T11:08:18

Build modules: apps/perl/5.16.1/gcc-4.4.6, apps/samtools/0.1.18/gcc-4.4.6, apps/cpanminus/1.5017/noarch

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

apps/perl/5.16.1/gcc-4.4.6 (using: apps/perl/5.16.1/gcc-4.4.6)

apps/samtools/0.1.18/gcc-4.4.6 (using: apps/samtools/0.1.18/gcc-4.4.6)

 

For further information, execute:

 

module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

 

module-prereq libs/gcc/system

module-prereq apps/perl/5.16.1/gcc-4.4.6

module-prereq apps/samtools/0.1.18/gcc-4.4.6

module-conflict apps/mitoseek

setenv MITOSEEKDIR /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18

setenv MITOSEEKBIN /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/bin

setenv MITOSEEKDOC /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/doc

prepend-path PERL5LIB /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/lib/perl5

prepend-path MANPATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/man

prepend-path PATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/bin

prepend-path PATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

 

HPC – Lampredi – software update – FASTX-Toolkit 0.0.13

 Uncategorized  No Responses »
Feb 242014
 

FASTX-Toolkit 0.0.13 has been added to the cluster (24/02/2014)

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
http://hannonlab.cshl.edu/fastx_toolkit/
-------------------------------------------------------------------

$ module load apps/fastx

apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

| — libs/gcc/system … SKIPPED (already loaded)

OK

$ ls $FASTXDIR

bin  share

ls $FASTXBIN

fasta_clipping_histogram.pl     fastx_barcode_splitter.pl

fasta_formatter                 fastx_clipper

fasta_nucleotide_changer        fastx_collapser

fastq_masker                    fastx_nucleotide_distribution_graph.sh

fastq_quality_boxplot_graph.sh  fastx_nucleotide_distribution_line_graph.sh

fastq_quality_converter         fastx_quality_stats

fastq_quality_filter            fastx_renamer

fastq_quality_trimmer           fastx_reverse_complement

fastq_to_fasta                  fastx_trimmer

fastx_artifacts_filter          fastx_uncollapser

——————————————————————-

$ module whatis apps/fastx

apps/fastx :
Title: fastx

Summary: A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

License: AGPLv3+

Group: Bioinformatics

URL: http://hannonlab.cshl.edu/fastx_toolkit/

Name: fastx

Version: 0.0.13

Module: apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Module path: /opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Package path: /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

 

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastx/0.0.13@3f151052

Last update: 2012-09-09

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:52

Build modules: libs/gtextutils/0.6/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

 

For further information, execute:

module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

——————————————————————-

$ module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

 

———– Module Specific Help for ‘apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6’ —————————

 

 

======== fastx ========

A collection of command line tools for Short-Reads

FASTA/FASTQ files preprocessing

======================

 

This module sets up your environment for the use of the ‘fastx’

application. This module sets up version ‘0.0.13’ of the

application.

 

 

>> SYNOPSIS <<

 

The FASTX-Toolkit is a collection of command line tools for

Short-Reads FASTA/FASTQ files preprocessing.

 

Next-Generation sequencing machines usually produce FASTA or FASTQ

files, containing multiple short-reads sequences (possibly with

quality information).

 

The main processing of such FASTA/FASTQ files is mapping (aka

aligning) the sequences to reference genomes or other databases

using specialized programs. Example of such mapping programs are:

Blat, SHRiMP, LastZ, MAQ and many many others.

 

However, it is sometimes more productive to preprocess the

FASTA/FASTQ files before mapping the sequences to the genome –

manipulating the sequences to produce better mapping results. The

FASTX-Toolkit tools perform some of these preprocessing tasks.

 

 

>> LICENSING <<

 

This package is made available subject to the following license(s):

 

AGPLv3+

 

Please refer to the website for further details regarding licensing.

 

 

>> FURTHER INFORMATION <<

 

More information about this software can be found at the website:

 

http://hannonlab.cshl.edu/fastx_toolkit/

 

For further details regarding this module, including the environment

modifications it will apply, execute:

 

module show apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

 

 

>> GET STARTED <<

 

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

package.

——————————————————————-

$ module show apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

/opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6:

module-whatis

 

Title: fastx

Summary: A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

License: AGPLv3+

Group: Bioinformatics

URL: http://hannonlab.cshl.edu/fastx_toolkit/

 

Name: fastx

Version: 0.0.13

Module: apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Module path: /opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Package path: /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

 

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastx/0.0.13@3f151052

Last update: 2012-09-09

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:52

Build modules: libs/gtextutils/0.6/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

 

For further information, execute:

module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

 

module-prereq libs/gcc/system

module-conflict apps/fastx

setenv FASTXDIR /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

setenv FASTXBIN /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/bin

setenv FASTXLIB /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/lib

prepend-path GDFONTPATH /usr/share/fonts/dejavu

setenv GNUPLOT_DEFAULT_GDFONT DejaVuSans

prepend-path PATH /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/bin

prepend-path LD_LIBRARY_PATH /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/lib

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – FASTQC 0.10.1

 Uncategorized  No Responses »
Feb 242014
 

FASTQC 0.10.1, a quality control tool for high throughput sequence data, has been added to the cluster (24/02/2014)

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

  • Import of data from BAM, SAM or FastQ files (any variant)
  • Providing a quick overview to tell you in which areas there may be problems
  • Summary graphs and tables to quickly assess your data
  • Export of results to an HTML based permanent report
  • Offline operation to allow automated generation of reports without running the interactive application

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

---------------------------------------------------------------------------------

$ module load apps/fastqc

apps/fastqc/0.10.1/noarch

|

OK

$ ls $FASTQCDIR

app  bin  doc

$ fastqc –version

FastQC v0.10.1

———————————————————————————

$ module whatis apps/fastqc

apps/fastqc          :

 

Title: FastQC

Summary: A quality control tool for high throughput sequence data

License: GPLv3+

Group: Bioinformatics

URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

Name: fastqc

Version: 0.10.1

Module: apps/fastqc/0.10.1/noarch

Module path: /opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch

Package path: /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

 

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastqc/0.10.1@0380e731

Last update: 2012-10-31

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:03

Compiler: N/A

 

For further information, execute:

module help apps/fastqc/0.10.1/noarch

 

———————————————————————————

$ module help apps/fastqc/0.10.1/noarch

 

———– Module Specific Help for ‘apps/fastqc/0.10.1/noarch’ —————————

 

 

======== FastQC ========

A quality control tool for high throughput sequence data

=======================

 

This module sets up your environment for the use of the ‘fastqc’

application. This module sets up version ‘0.10.1’ of the

application.

 

 

>> SYNOPSIS <<

 

FastQC aims to provide a simple way to do some quality control

checks on raw sequence data coming from high throughput sequencing

pipelines. It provides a modular set of analyses which you can use

to give a quick impression of whether your data has any problems of

which you should be aware before doing any further analysis.

 

The main functions of FastQC are:

 

* Import of data from BAM, SAM or FastQ files (any variant)

* Providing a quick overview to tell you in which areas there may

be problems

* Summary graphs and tables to quickly assess your data

* Export of results to an HTML based permanent report

* Offline operation to allow automated generation of reports

without running the interactive application

 

 

>> LICENSING <<

 

This package is made available subject to the following license(s):

 

GPLv3+

 

Please refer to the website for further details regarding licensing.

 

 

>> FURTHER INFORMATION <<

 

More information about this software can be found at the website:

 

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

For further details regarding this module, including the environment

modifications it will apply, execute:

 

module show apps/fastqc/0.10.1/noarch

 

 

>> GET STARTED <<

 

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

package.

———————————————————————————

$ module show apps/fastqc/0.10.1/noarch

 

/opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch:

 

module-whatis

 

Title: FastQC

Summary: A quality control tool for high throughput sequence data

License: GPLv3+

Group: Bioinformatics

URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

Name: fastqc

Version: 0.10.1

Module: apps/fastqc/0.10.1/noarch

Module path: /opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch

Package path: /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

 

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastqc/0.10.1@0380e731

Last update: 2012-10-31

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:03

Compiler: N/A

 

 

For further information, execute:

 

module help apps/fastqc/0.10.1/noarch

 

module-conflict apps/fastqc

setenv FASTQCDIR /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

setenv FASTQCBIN /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/bin

setenv FASTQCAPP /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/app

setenv FASTQCDOC /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/doc

prepend-path PATH /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/bin

———————————————————————————

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – LoFreq 0.6.1

 Uncategorized  No Responses »
Feb 242014
 

LoFreq 0.6.1 was added to the cluster (05/12/2013)

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

http://sourceforge.net/p/lofreq/wiki/Home/

——————————————————————-

$ module load apps/lofreq
apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
| — libs/gcc/system
| * –> OK
| — apps/python/2.7.3/gcc-4.4.6
| | — libs/gcc/system … SKIPPED (already loaded)
| * –> OK
|
OK

$ ls $LOFREQDIR
bin python

$ ls $LOFREQBIN
base_qual_calib_wrapper.sh lofreq_bonf.py lofreq_pileup_summary.py lofreq_snpcaller.py lofreq_varpos_to_vcf.py
bwa_unique.sh lofreq_diff.py lofreq_regionbed.py lofreq_uniq_pipeline.py lofreq_version.py
lofreq_alnoffset.py lofreq_filter.py lofreq_samtools lofreq_uniq.py

——————————————————————-

$ module whatis apps/lofreq
apps/lofreq :

Title: LoFreq
Summary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
License: BSD License
Group: Bioinformatics
URL: http://sourceforge.net/p/lofreq/wiki/Home/

Name: lofreq
Version: 0.6.1
Module: apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Module path: /opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Package path: /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-12-05T16:00:29
Build modules: apps/python/2.7.3/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/python/2.7.3/gcc-4.4.6 (using: apps/python/2.7.3/gcc-4.4.6)

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

——————————————————————-

$ module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

———– Module Specific Help for ‘apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3’ —————————

======== LoFreq ========
fast and sensitive variant-caller for inferring SNVs from
high-throughput sequencing data
=======================

This module sets up your environment for the use of the ‘lofreq’
application. This module sets up version ‘0.6.1’ of the
application.

>> SYNOPSIS << LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly call low-frequency variants by exploiting base-call quality values. LoFreq has been used to call rare variants in viral and bacterial sequencing datasets and can be used to study mitochondrial heteroplasmy and rare somatic mutations in heterogeneous tumors. LoFreq makes full use of base-call qualities (and versions >=0.5
also use read mapping qualities) which are usually ignored by other
methods or only used for filtering. It is very sensitive; most
notably, it is able to predict variants below the average base-call
quality (i.e. sequencing error rate). Each SNV call is assigned a
p-value which allows for rigorous false positive control. Even
though it uses no approximations or heuristics, it is very efficient
due to several runtime optimizations. LoFreq is generic and fast
enough to be applied to high-coverage data and large genomes. It
takes a minute to analyze Dengue genome sequencing data with nearly
4000X coverage, roughly one hour to call SNVs on a 600X coverage
E.coli genome and 1.5 hours to run on a 100X coverage human exome
dataset.

>> LICENSING << This package is made available subject to the following license(s): BSD License Please refer to the website for further details regarding licensing. >> FURTHER INFORMATION << More information about this software can be found at the website: http://sourceforge.net/p/lofreq/wiki/Home/ For further details regarding this module, including the environment modifications it will apply, execute: module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3 >> GET STARTED <<

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

——————————————————————-

$ module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
——————————————————————-
/opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3:

module-whatis

Title: LoFreq
Summary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
License: BSD License
Group: Bioinformatics
URL: http://sourceforge.net/p/lofreq/wiki/Home/

Name: lofreq
Version: 0.6.1
Module: apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Module path: /opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Package path: /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-12-05T16:00:29
Build modules: apps/python/2.7.3/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/python/2.7.3/gcc-4.4.6 (using: apps/python/2.7.3/gcc-4.4.6)

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

module-prereq libs/gcc/system
module-prereq apps/python/2.7.3/gcc-4.4.6
module-conflict apps/lofreq
setenv LOFREQDIR /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
setenv LOFREQBIN /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
setenv LOFREQPYTHON /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python
prepend-path PATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
prepend-path PYTHONPATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python/lib/python2.7/site-packages

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – MuTect 1.1.4

 Uncategorized  No Responses »
Oct 312013
 

MuTect 1.1.4 has been added to the cluster (31/10/2013)

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

——————————————————————-
$ module load apps/mutect
apps/mutect/1.1.4/bin
|
OK

$ ls $MUTECTDIR
bin doc java

$ ls $MUTECTDIR/*
/opt/gridware/pkg/apps/mutect/1.1.4/bin/bin:
mutect muTect

/opt/gridware/pkg/apps/mutect/1.1.4/bin/doc:
LICENSE.TXT version.txt

/opt/gridware/pkg/apps/mutect/1.1.4/bin/java:
muTect.jar

$ mutect
---------------------------------------------------------------------------------
The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02
Copyright (c) 2010 The Broad Institute
For support and documentation go to http://www.broadinstitute.org/gatk
---------------------------------------------------------------------------------
---------------------------------------------------------------------------------
usage: java -jar muTect.jar -T [-args ] [-I ] [-rbs ] [-et
] [-K ] [-tag ] [-rf ] [-L ] [-XL ] [-isr
] [-im ] [-ip ] [-R ] [-ndrs]
[--disableRandomization] [-maxRuntime ] [-maxRuntimeUnits ] [-dt ]
[-dfrac ] [-dcov ] [-baq ] [-baqGOP ] [-PF
] [-OQ] [-BQSR ] [-DIQ] [-EOQ] [-preserveQ ] [-DBQ
] [-S ] [-rpr] [-kpr] [-U ] [-nt ] [-nct
] [-mte] [-bfh ] [-rgbl ] [-ped
] [-pedString ] [-pedValidationType ] [-l ] [-log
] [-h]

-T,--analysis_type Type of analysis to run

[snip]

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
##### ERROR ------------------------------------------------------------------------------------------

——————————————————————-

$ module whatis apps/mutect
apps/mutect :

Title: MuTect
Summary: Reliable and accurate identification of somatic point mutations
License: NONFREE - Free for academic non-commercial research purposes only; see http://j.mp/10q7Mmv
Group: Bioinformatics
URL: http://www.broadinstitute.org/cancer/cga/mutect

Name: mutect
Version: 1.1.4
Module: apps/mutect/1.1.4/bin
Module path: /opt/gridware/etc/modules/apps/mutect/1.1.4/bin
Package path: /opt/gridware/pkg/apps/mutect/1.1.4/bin

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/mutect/@3956ddde
Last update: 2013-04-03

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:42:07
Build parameters: zipfile=/opt/gridware/ext/muTect-1.1.4-bin.zip
Compiler: N/A

For further information, execute:

module help apps/mutect/1.1.4/bin

——————————————————————-

$ module help apps/mutect/1.1.4/bin

----------- Module Specific Help for 'apps/mutect/1.1.4/bin' ---------------------------

======== MuTect ========
Reliable and accurate identification of somatic point
mutations
=======================

This module sets up your environment for the use of the 'mutect'
application. This module sets up version '1.1.4' 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/mutect/1.1.4/bin
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/mutect/1.1.4/bin

module-whatis

Title: MuTect
Summary: Reliable and accurate identification of somatic point mutations
License: NONFREE - Free for academic non-commercial research purposes only; see http://j.mp/10q7Mmv
Group: Bioinformatics
URL: http://www.broadinstitute.org/cancer/cga/mutect

Name: mutect
Version: 1.1.4
Module: apps/mutect/1.1.4/bin
Module path: /opt/gridware/etc/modules/apps/mutect/1.1.4/bin
Package path: /opt/gridware/pkg/apps/mutect/1.1.4/bin

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/mutect/@3956ddde
Last update: 2013-04-03

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:42:07
Build parameters: zipfile=/opt/gridware/ext/muTect-1.1.4-bin.zip
Compiler: N/A

For further information, execute:

module help apps/mutect/1.1.4/bin

module-conflict apps/mutect
setenv MUTECTDIR /opt/gridware/pkg/apps/mutect/1.1.4/bin
setenv MUTECTBIN /opt/gridware/pkg/apps/mutect/1.1.4/bin/bin
setenv MUTECTDOC /opt/gridware/pkg/apps/mutect/1.1.4/bin/doc
setenv MUTECTJAVA /opt/gridware/pkg/apps/mutect/1.1.4/bin/java
setenv MUTECT_JAVA_MEM_MX 2g
setenv MUTECT_JAVA_TMPDIR /tmp
setenv MUTECT_JAVA_OPTS -Xmx$MUTECT_JAVA_MEM_MX -Djava.io.tmpdir=$MUTECT_JAVA_TMPDIR
prepend-path PATH /opt/gridware/pkg/apps/mutect/1.1.4/bin/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – Strelka 1.0.12

 Uncategorized  No Responses »
Oct 312013
 

Strelka 1.0.12 has been added to the cluster (31/10/2013)

This is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

——————————————————————-

$ module load apps/strelka
apps/strelka/1.0.12/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

$ ls $STRELKADIR/
bin etc lib libexec opt

$ ls $STRELKADIR/*
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin:
configureStrelkaWorkflow.pl demo

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/etc:
strelka_config_bwa_default.ini strelka_config_eland_default.ini strelka_config_isaac_default.ini

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/lib:
Utils.pm

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec:
callSomaticVariants.pl consolidateResults.pl countFastaBases filterSomaticVariants.pl strelka2

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/opt:
Makefile samtools-0.1.18_no_tview vcftools vcftools-r837.tar.gz
samtools samtools-0.1.18_no_tview.tar.bz2 vcftools-r837

$ $STRELKABIN/demo/run_demo.bash

**** Starting demo configuration.
**** Configuration cmd: '/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/../configureStrelkaWorkflow.pl --tumor=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/NA12891_dupmark_chr20_region.bam --normal=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/NA12892_dupmark_chr20_region.bam --ref=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/chr20_860k_only.fa --config=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/strelka_demo_config.ini --output-dir=./strelkaDemoAnalysis'

INFO: Scanning reference genome
INFO: Scanning reference genome complete

Successfully configured analysis and created makefile '/users/alces-cluster/strelkaDemoAnalysis/Makefile'.

To run the analysis locally using make, run:

make -C /users/alces-cluster/strelkaDemoAnalysis

...or:

cd /users/alces-cluster/strelkaDemoAnalysis
make

**** Completed demo configuration.

**** Starting demo workflow execution.
**** Workflow cmd: 'make -C ./strelkaDemoAnalysis'

make: Entering directory `/users/alces-cluster/strelkaDemoAnalysis'
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0001 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0001/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0002 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0002/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0000 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0000/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/filterSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/consolidateResults.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini && touch /users/alces-cluster/strelkaDemoAnalysis/task.complete

Analysis complete. Final somatic calls can be found in /users/alces-cluster/strelkaDemoAnalysis/results

make: Leaving directory `/users/alces-cluster/strelkaDemoAnalysis'

**** Completed demo workflow execution.

**** Starting comparison to expected results.
**** Expected results dir: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/expected_results
**** Demo results dir: ./strelkaDemoAnalysis/results

**** No differences between expected and computed results.

**** Demo/verification successfully completed

——————————————————————-

$ module whatis apps/strelka
apps/strelka :

Title: Strelka
Summary: Somatic variant calling workflow for matched tumor-normal samples
License: NONFREE - Illumina Open Source Source License
Group: Bioinformatics
URL: https://sites.google.com/site/strelkasomaticvariantcaller/

Name: strelka
Version: 1.0.12
Module: apps/strelka/1.0.12/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/strelka/@f8d32f14
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:46:53
Build parameters: tarball=/opt/gridware/ext/strelka_workflow-1.0.12.tar.gz
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/strelka/1.0.12/gcc-4.4.6

——————————————————————-

$ module help apps/strelka/1.0.12/gcc-4.4.6

----------- Module Specific Help for 'apps/strelka/1.0.12/gcc-4.4.6' ---------------------------

======== Strelka ========
Somatic variant calling workflow for matched tumor-normal
samples
========================

This module sets up your environment for the use of the 'strelka'
application. This module sets up version '1.0.12' 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/strelka/1.0.12/gcc-4.4.6
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6:

module-whatis

Title: Strelka
Summary: Somatic variant calling workflow for matched tumor-normal samples
License: NONFREE - Illumina Open Source Source License
Group: Bioinformatics
URL: https://sites.google.com/site/strelkasomaticvariantcaller/

Name: strelka
Version: 1.0.12
Module: apps/strelka/1.0.12/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/strelka/@f8d32f14
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:46:53
Build parameters: tarball=/opt/gridware/ext/strelka_workflow-1.0.12.tar.gz
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/strelka/1.0.12/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/strelka
setenv STRELKADIR /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6
setenv STRELKABIN /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin
prepend-path PATH /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin


——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – FamSeq 1.0.0-2

 Uncategorized  No Responses »
Oct 282013
 

FamSeq 1.0.0-2 has been added to lampredi2. Details are:

$ module load apps/famseq
apps/famseq/1.0.0-2/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

[...@node05(lampredi) ~]$ ls $FAMSEQDIR
bin doc sample

[...@node05(lampredi) ~]$ ls $FAMSEQDIR/doc
manual.pdf

[...@node05(lampredi) ~]$ FamSeq

Program: FamSeq (Sequence calling using pedigree information)
Version: 0.0.1

Usage: FamSeq [options]

Input type: vcf input vcf file
LK input likelihood file

——————————————————————-

$ module whatis apps/famseq
apps/famseq :

Title: FamSeq
Summary: A computational tool for calculating probability of variants in family-based sequencing data
License: Public Domain
Group: Bioinformatics
URL: http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html

Name: famseq
Version: 1.0.0-2
Module: apps/famseq/1.0.0-2/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/famseq/1.0.0-2@61f6fd9a
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:52:15
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/famseq/1.0.0-2/gcc-4.4.6

——————————————————————-

$ module help apps/famseq/1.0.0-2/gcc-4.4.6

----------- Module Specific Help for 'apps/famseq/1.0.0-2/gcc-4.4.6' ---------------------------

======== FamSeq ========
A computational tool for calculating probability of
variants in family-based sequencing data
=======================

This module sets up your environment for the use of the 'famseq'
application. This module sets up version '1.0.0-2' 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/famseq/1.0.0-2/gcc-4.4.6
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6:

module-whatis

Title: FamSeq
Summary: A computational tool for calculating probability of variants in family-based sequencing data
License: Public Domain
Group: Bioinformatics
URL: http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html

Name: famseq
Version: 1.0.0-2
Module: apps/famseq/1.0.0-2/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/famseq/1.0.0-2@61f6fd9a
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:52:15
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/famseq/1.0.0-2/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/famseq
setenv FAMSEQDIR /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6
setenv FAMSEQBIN /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/bin
setenv FAMSEQDOC /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/doc
setenv FAMSEQSAMPLE /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/sample
prepend-path PATH /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

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