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