{"id":276,"date":"2013-10-31T14:05:23","date_gmt":"2013-10-31T14:05:23","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=276"},"modified":"2013-10-31T14:37:41","modified_gmt":"2013-10-31T14:37:41","slug":"hpc-lampredi-software-update-strelka-1-0-12","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=276","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 Strelka 1.0.12"},"content":{"rendered":"

Strelka 1.0.12 has been added to the cluster (31\/10\/2013)<\/p>\n

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

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module load apps\/strelka
\napps\/strelka\/1.0.12\/gcc-4.4.6
\n | -- libs\/gcc\/system
\n | * --> OK
\n |
\n OK<\/p>\n

$ ls $STRELKADIR\/
\nbin etc lib libexec opt<\/p>\n

$ ls $STRELKADIR\/*
\n\/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/bin:
\nconfigureStrelkaWorkflow.pl demo<\/p>\n

\/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/etc:
\nstrelka_config_bwa_default.ini strelka_config_eland_default.ini strelka_config_isaac_default.ini<\/p>\n

\/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/lib:
\nUtils.pm<\/p>\n

\/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/libexec:
\ncallSomaticVariants.pl consolidateResults.pl countFastaBases filterSomaticVariants.pl strelka2<\/p>\n

\/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/opt:
\nMakefile samtools-0.1.18_no_tview vcftools vcftools-r837.tar.gz
\nsamtools samtools-0.1.18_no_tview.tar.bz2 vcftools-r837<\/p>\n

$ $STRELKABIN\/demo\/run_demo.bash<\/p>\n

**** Starting demo configuration.
\n**** 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'<\/p>\n

INFO: Scanning reference genome
\nINFO: Scanning reference genome complete<\/p>\n

Successfully configured analysis and created makefile '\/users\/alces-cluster\/strelkaDemoAnalysis\/Makefile'.<\/p>\n

To run the analysis locally using make, run:<\/p>\n

make -C \/users\/alces-cluster\/strelkaDemoAnalysis<\/p>\n

...or:<\/p>\n

cd \/users\/alces-cluster\/strelkaDemoAnalysis
\nmake<\/p>\n

**** Completed demo configuration.<\/p>\n

**** Starting demo workflow execution.
\n**** Workflow cmd: 'make -C .\/strelkaDemoAnalysis'<\/p>\n

make: Entering directory `\/users\/alces-cluster\/strelkaDemoAnalysis'
\n\/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
\n\/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
\n\/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
\n\/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
\n\/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<\/p>\n

Analysis complete. Final somatic calls can be found in \/users\/alces-cluster\/strelkaDemoAnalysis\/results<\/p>\n

make: Leaving directory `\/users\/alces-cluster\/strelkaDemoAnalysis'<\/p>\n

**** Completed demo workflow execution.<\/p>\n

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

**** No differences between expected and computed results.<\/p>\n

**** Demo\/verification successfully completed
\n<\/code><\/p>\n

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module whatis apps\/strelka
\napps\/strelka : <\/p>\n

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

Name: strelka
\n Version: 1.0.12
\n Module: apps\/strelka\/1.0.12\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/strelka\/1.0.12\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6<\/p>\n

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

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

For further information, execute:<\/p>\n

\tmodule help apps\/strelka\/1.0.12\/gcc-4.4.6
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module help apps\/strelka\/1.0.12\/gcc-4.4.6<\/p>\n

----------- Module Specific Help for 'apps\/strelka\/1.0.12\/gcc-4.4.6' ---------------------------<\/p>\n

======== Strelka ========
\n Somatic variant calling workflow for matched tumor-normal
\n samples
\n ======================== <\/p>\n

This module sets up your environment for the use of the 'strelka'
\napplication. This module sets up version '1.0.12' of the
\napplication.<\/p>\n

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<<\/p>\n

Please refer to the website for further details on usage of this
\npackage.
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module show apps\/strelka\/1.0.12\/gcc-4.4.6
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/strelka\/1.0.12\/gcc-4.4.6:<\/p>\n

module-whatis\t <\/p>\n

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

Name: strelka
\n Version: 1.0.12
\n Module: apps\/strelka\/1.0.12\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/strelka\/1.0.12\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6<\/p>\n

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

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

For further information, execute:<\/p>\n

\tmodule help apps\/strelka\/1.0.12\/gcc-4.4.6<\/p>\n

module-prereq\t libs\/gcc\/system
\nmodule-conflict\t apps\/strelka
\nsetenv\t\t STRELKADIR \/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6
\nsetenv\t\t STRELKABIN \/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/bin
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/strelka\/1.0.12\/gcc-4.4.6\/bin <\/p>\n

<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

Lampredi HPC
\nigm-lampredi-users@ncl.ac.uk<\/p>\n

IGM IT
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"

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. \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014- $ 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 $ […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21,22],"class_list":["post-276","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","tag-linux","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/276","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=276"}],"version-history":[{"count":6,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/276\/revisions"}],"predecessor-version":[{"id":282,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/276\/revisions\/282"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=276"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=276"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}