{"id":206,"date":"2013-10-02T09:17:54","date_gmt":"2013-10-02T08:17:54","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=206"},"modified":"2013-10-02T09:32:14","modified_gmt":"2013-10-02T08:32:14","slug":"hpc-lampredi-software-update-gatk-gatkqueue","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=206","title":{"rendered":"HPC – Lampredi – software update – GATK & GATKQUEUE 2.7.2"},"content":{"rendered":"

GATK 2.7.2 and GATKQUEUE 2.7.2 have been added to lampredi2. Details are:<\/p>\n

$module load apps\/gatk\/2.7.2\/noarch
\napps\/gatk\/2.7.2\/noarch
\n |
\n OK<\/p>\n

$ ls $GATKDIR
\nbin GenomeAnalysisTK.jar resources<\/code><\/p>\n

———————————————————————————-<\/p>\n

$ module whatis apps\/gatk\/2.7.2\/noarch
\napps\/gatk\/2.7.2 : <\/p>\n

Title: Genome Analysis Toolkit
\n Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data
\n License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N
\n Group: Bioinformatics
\n URL: http:\/\/www.broadinstitute.org\/gatk\/index.php<\/p>\n

Name: gatk
\n Version: 2.7.2
\n Module: apps\/gatk\/2.7.2\/noarch
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/gatk\/2.7.2\/noarch
\n Package path: \/opt\/gridware\/pkg\/apps\/gatk\/2.7.2\/noarch<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: ext\/gatk\/2.7.2@9df24753
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T15:50:24
\n Build parameters: tarball=\/opt\/gridware\/ext\/GenomeAnalysisTK-2.7-2.tar.bz2
\n Compiler: N\/A<\/p>\n

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

\tmodule help apps\/gatk\/2.7.2\/noarch<\/code><\/p>\n

———————————————————————————-<\/p>\n

$ module help apps\/gatk\/2.7.2\/noarch<\/p>\n

----------- Module Specific Help for 'apps\/gatk\/2.7.2\/noarch' ---------------------------<\/p>\n

======== Genome Analysis Toolkit ========
\n Software package developed at the Broad Institute to
\n analyse next-generation resequencing data
\n ======================================== <\/p>\n

This module sets up your environment for the use of the 'gatk'
\napplication. This module sets up version '2.7.2' 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———————————————————————————-<\/p>\n

$ module show apps\/gatk\/2.7.2\/noarch
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/gatk\/2.7.2\/noarch:<\/p>\n

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

Title: Genome Analysis Toolkit
\n Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data
\n License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N
\n Group: Bioinformatics
\n URL: http:\/\/www.broadinstitute.org\/gatk\/index.php<\/p>\n

Name: gatk
\n Version: 2.7.2
\n Module: apps\/gatk\/2.7.2\/noarch
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/gatk\/2.7.2\/noarch
\n Package path: \/opt\/gridware\/pkg\/apps\/gatk\/2.7.2\/noarch<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: ext\/gatk\/2.7.2@9df24753
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T15:50:24
\n Build parameters: tarball=\/opt\/gridware\/ext\/GenomeAnalysisTK-2.7-2.tar.bz2
\n Compiler: N\/A<\/p>\n

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

\tmodule help apps\/gatk\/2.7.2\/noarch<\/p>\n

module-conflict\t apps\/gatk
\nmodule-conflict\t apps\/gatklite
\nsetenv\t\t GATKDIR \/opt\/gridware\/pkg\/apps\/gatk\/2.7.2\/noarch
\nsetenv\t\t GATKBIN \/opt\/gridware\/pkg\/apps\/gatk\/2.7.2\/noarch\/bin
\nsetenv\t\t GATK_JAVA_MEM_MX 2g
\nsetenv\t\t GATK_JAVA_TMPDIR \/tmp
\nsetenv\t\t GATK_JAVA_OPTS -Xmx$GATK_JAVA_MEM_MX -Djava.io.tmpdir=$GATK_JAVA_TMPDIR
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/gatk\/2.7.2\/noarch\/bin <\/code>
\n——————————————————————-<\/p>\n

GATKQUEUE 2.7.2<\/p>\n

$ module load apps\/gatkqueue\/2.7.2\/noarch
\napps\/gatkqueue\/2.7.2\/noarch
\n | -- apps\/gatk\/2.7.2\/noarch
\n | * --> OK
\n |
\n OK<\/p>\n

$ ls $GATKQUEUEDIR
\nbin java Queue.jar resources<\/code><\/p>\n

———————————————————————————-<\/p>\n

$ module whatis apps\/gatkqueue\/2.7.2\/noarch
\napps\/gatkqueue\/2.7.2\/noarch: <\/p>\n

Title: Genome Analysis Toolkit Queue
\n Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines
\n License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N
\n Group: Bioinformatics
\n URL: http:\/\/www.broadinstitute.org\/gatk\/index.php<\/p>\n

Name: gatkqueue
\n Version: 2.7.2
\n Module: apps\/gatkqueue\/2.7.2\/noarch
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/2.7.2\/noarch
\n Package path: \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: ext\/gatkqueue\/2.7.2@95ff256d
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T15:50:50
\n Build parameters: tarball=\/opt\/gridware\/ext\/Queue-2.7-2.tar.bz2
\n Compiler: N\/A
\n Dependencies: apps\/gatk\/2.7.2\/noarch (using: apps\/gatk\/2.7.2\/noarch)<\/p>\n

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

\tmodule help apps\/gatkqueue\/2.7.2\/noarch<\/code><\/p>\n

———————————————————————————-<\/p>\n

$ module help apps\/gatkqueue\/2.7.2\/noarch<\/p>\n

----------- Module Specific Help for 'apps\/gatkqueue\/2.7.2\/noarch' ---------------------------<\/p>\n

======== Genome Analysis Toolkit Queue ========
\n Command-line scripting framework for defining multi-stage
\n genomic analysis pipelines
\n ============================================== <\/p>\n

This module sets up your environment for the use of the 'gatkqueue'
\napplication. This module sets up version '2.7.2' 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———————————————————————————-<\/p>\n

$ module show apps\/gatkqueue\/2.7.2\/noarch
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/2.7.2\/noarch:<\/p>\n

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

Title: Genome Analysis Toolkit Queue
\n Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines
\n License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N
\n Group: Bioinformatics
\n URL: http:\/\/www.broadinstitute.org\/gatk\/index.php<\/p>\n

Name: gatkqueue
\n Version: 2.7.2
\n Module: apps\/gatkqueue\/2.7.2\/noarch
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/2.7.2\/noarch
\n Package path: \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: ext\/gatkqueue\/2.7.2@95ff256d
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T15:50:50
\n Build parameters: tarball=\/opt\/gridware\/ext\/Queue-2.7-2.tar.bz2
\n Compiler: N\/A
\n Dependencies: apps\/gatk\/2.7.2\/noarch (using: apps\/gatk\/2.7.2\/noarch)<\/p>\n

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

\tmodule help apps\/gatkqueue\/2.7.2\/noarch<\/p>\n

module-prereq\t apps\/gatk\/2.7.2\/noarch
\nmodule-conflict\t apps\/gatkqueue
\nsetenv\t\t GATKQUEUEDIR \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch
\nsetenv\t\t GATKQUEUEEXAMPLES \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch\/resources
\nsetenv\t\t GATKQUEUEBIN \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch\/bin
\nsetenv\t\t GATKQUEUE_JAVA_MEM_MX 2g
\nsetenv\t\t GATKQUEUE_JAVA_TMPDIR \/tmp
\nsetenv\t\t GATKQUEUE_JAVA_OPTS -Xmx$GATKQUEUE_JAVA_MEM_MX -Djava.io.tmpdir=$GATKQUEUE_JAVA_TMPDIR
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/gatkqueue\/2.7.2\/noarch\/bin <\/code>
\n——————————————————————-<\/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":"

GATK 2.7.2 and GATKQUEUE 2.7.2 have been added to lampredi2. Details are: $module load apps\/gatk\/2.7.2\/noarch apps\/gatk\/2.7.2\/noarch | OK $ ls $GATKDIR bin GenomeAnalysisTK.jar resources ———————————————————————————- $ module whatis apps\/gatk\/2.7.2\/noarch apps\/gatk\/2.7.2 : Title: Genome Analysis Toolkit Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data License: Free for non-commercial use; registration required; […]<\/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],"class_list":["post-206","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","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\/206","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=206"}],"version-history":[{"count":11,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/206\/revisions"}],"predecessor-version":[{"id":218,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/206\/revisions\/218"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=206"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=206"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=206"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}