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