{"id":395,"date":"2014-04-14T12:39:35","date_gmt":"2014-04-14T11:39:35","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=395"},"modified":"2014-04-14T12:42:48","modified_gmt":"2014-04-14T11:42:48","slug":"hpc-lampredi-software-update-gatk-and-gatk-queue-3-1-1","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=395","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 GATK and GATK Queue 3.1.1"},"content":{"rendered":"<pre>\r\n$ module load apps\/gatk\/3.1.1\/noarch\r\napps\/gatk\/3.1.1\/noarch\r\n |\r\n OK\r\n\r\n$ ls $GATKDIR\r\nbin  GenomeAnalysisTK.jar  Queue.jar  resources\r\n\r\n$ ls $GATKBIN\r\ngatk                              gatk_ErrorThrowing                 gatk_ReadBackedPhasing\r\ngatk_AnalyzeCovariates            gatk_FastaAlternateReferenceMaker  gatk_ReadClippingStats\r\ngatk_ApplyRecalibration           gatk_FastaReferenceMaker           gatk_ReadGroupProperties\r\ngatk_BaseCoverageDistribution     gatk_FastaStats                    gatk_ReadLengthDistribution\r\ngatk_BaseRecalibrator             gatk_FilterLiftedVariants          gatk_RealignerTargetCreator\r\ngatk_BeagleOutputToVCF            gatk_FindCoveredIntervals          gatk_RegenotypeVariants\r\ngatk_CalculateGenotypePosteriors  gatk_FlagStat                      gatk_SelectHeaders\r\ngatk_CallableLoci                 gatk_GATKPaperGenotyper            gatk_SelectVariants\r\ngatk_CheckAlignment               gatk_GCContentByInterval           gatk_SimulateReadsForVariants\r\ngatk_CheckPileup                  gatk_GenotypeAndValidate           gatk_SplitNCigarReads\r\ngatk_ClipReads                    gatk_GenotypeConcordance           gatk_SplitSamFile\r\ngatk_CombineGVCFs                 gatk_GenotypeGVCFs                 gatk_UnifiedGenotyper\r\ngatk_CombineVariants              gatk_HaplotypeCaller               gatk_ValidateVariants\r\ngatk_CompareCallableLoci          gatk_HaplotypeResolver             gatk_ValidationAmplicons\r\ngatk_CountBases                   gatk_IndelRealigner                gatk_ValidationSiteSelector\r\ngatk_CountIntervals               gatk_LeftAlignAndTrimVariants      gatk_VariantAnnotator\r\ngatk_CountLoci                    gatk_LeftAlignIndels               gatk_VariantEval\r\ngatk_CountMales                   gatk_LiftoverVariants              gatk_VariantFiltration\r\ngatk_CountReadEvents              gatk_PhaseByTransmission           gatk_VariantRecalibrator\r\ngatk_CountReads                   gatk_Pileup                        gatk_VariantsToAllelicPrimitives\r\ngatk_CountRODs                    gatk_PrintReads                    gatk_VariantsToBeagleUnphased\r\ngatk_CountRODsByRef               gatk_PrintRODs                     gatk_VariantsToBinaryPed\r\ngatk_CountTerminusEvent           gatk_ProduceBeagleInput            gatk_VariantsToTable\r\ngatk_CoveredByNSamplesSites       gatk_QCRef                         gatk_VariantsToVCF\r\ngatk_DepthOfCoverage              gatk_QualifyMissingIntervals       gatk_VariantValidationAssessor\r\ngatk_DiagnoseTargets              gatk-queue                         GenomeAnalysisTK\r\ngatk_DiffObjects                  gatk_RandomlySplitVariants         Queue\r\ngatk_ErrorRatePerCycle            gatk_ReadAdaptorTrimmer\r\n\r\n<\/pre>\n<pre>\r\n$ module show apps\/gatk\/3.1.1\/noarch\r\n-------------------------------------------------------------------\r\n\/opt\/gridware\/etc\/modules\/apps\/gatk\/3.1.1\/noarch:\r\n\r\nmodule-whatis\t \r\n\r\n            Title: Genome Analysis Toolkit + Queue\r\n          Summary: Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines\r\n          License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/gatk\/index.php\r\n\r\n             Name: gatk\r\n          Version: 3.1.1\r\n           Module: apps\/gatk\/3.1.1\/noarch\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/gatk\/3.1.1\/noarch\r\n     Package path: \/opt\/gridware\/pkg\/apps\/gatk\/3.1.1\/noarch\r\n\r\n       Repository: file:\/opt\/gridware\/etc\/repos\/local\r\n          Package: ext\/gatk+queue\/3.x@05599477\r\n      Last update: 2014-04-14\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-04-14T10:58:33\r\n 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\r\n         Compiler: N\/A\r\n\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/gatk\/3.1.1\/noarch\r\n \r\nmodule-conflict\t apps\/gatk \r\nmodule-conflict\t apps\/gatklite \r\nsetenv\t\t GATKDIR \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch \r\nsetenv\t\t GATKBIN \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch\/bin \r\nsetenv\t\t GATK_JAVA_MEM_MX 2g \r\nsetenv\t\t GATK_JAVA_TMPDIR \/tmp \r\nsetenv\t\t GATK_JAVA_OPTS -Xmx$GATK_JAVA_MEM_MX -Djava.io.tmpdir=$GATK_JAVA_TMPDIR \r\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch\/bin \r\n-------------------------------------------------------------------\r\n<\/pre>\n<pre>\r\n$ whatis apps\/gatk\/3.1.1\/noarch\r\napps\/gatk\/3.1.1\/noarch: nothing appropriate\r\n[nas18@login1(lampredi) ~]$ module whatis apps\/gatk\/3.1.1\/noarch\r\napps\/gatk\/3.1.1\/noarch: \r\n\r\n            Title: Genome Analysis Toolkit + Queue\r\n          Summary: Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines\r\n          License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/gatk\/index.php\r\n\r\n             Name: gatk\r\n          Version: 3.1.1\r\n           Module: apps\/gatk\/3.1.1\/noarch\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/gatk\/3.1.1\/noarch\r\n     Package path: \/opt\/gridware\/pkg\/apps\/gatk\/3.1.1\/noarch\r\n\r\n       Repository: file:\/opt\/gridware\/etc\/repos\/local\r\n          Package: ext\/gatk+queue\/3.x@05599477\r\n      Last update: 2014-04-14\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-04-14T10:58:33\r\n 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\r\n         Compiler: N\/A\r\n\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/gatk\/3.1.1\/noarch\r\n<\/pre>\n<pre>\r\n$ module help apps\/gatk\/3.1.1\/noarch\r\n\r\n----------- Module Specific Help for 'apps\/gatk\/3.1.1\/noarch' ---------------------------\r\n\r\n\r\n          ======== Genome Analysis Toolkit + Queue ========          \r\n       Broad Institute package for analysing next-generation        \r\n        resequencing data; including command-line scripting         \r\n        framework for defining multi-stage genomic analysis         \r\n                              pipelines                              \r\n          ================================================          \r\n\r\nThis module sets up your environment for the use of the 'gatk'\r\napplication. This module sets up version '3.1.1' of the\r\napplication.\r\n\r\n\r\n&gt;&gt; SYNOPSIS &lt;&gt; LICENSING &lt;&gt; FURTHER INFORMATION &lt;&gt; GET STARTED &lt;&lt;\r\n\r\nPlease refer to the website for further details on usage of this\r\npackage.\r\n<\/pre>\n<pre>\r\n$ module load apps\/gatkqueue\/3.1.1\/noarch\r\napps\/gatkqueue\/3.1.1\/noarch\r\n |\r\n OK\r\n<\/pre>\n<pre>\r\n$ module show apps\/gatkqueue\/3.1.1\/noarch\r\n-------------------------------------------------------------------\r\n\/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/3.1.1\/noarch:\r\n\r\nmodule-whatis\t \r\n\r\n            Title: Genome Analysis Toolkit + Queue\r\n          Summary: Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines\r\n          License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/gatk\/index.php\r\n\r\n             Name: gatkqueue\r\n          Version: 3.1.1\r\n           Module: apps\/gatkqueue\/3.1.1\/noarch\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/3.1.1\/noarch\r\n     Package path: \/opt\/gridware\/pkg\/apps\/gatkqueue\/3.1.1\/noarch\r\n\r\n       Repository: file:\/opt\/gridware\/etc\/repos\/local\r\n          Package: ext\/gatk+queue\/3.x@05599477\r\n      Last update: 2014-04-14\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-04-14T10:58:34\r\n 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\r\n         Compiler: N\/A\r\n\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/gatkqueue\/3.1.1\/noarch\r\n \r\nmodule-conflict\t apps\/gatkqueue \r\nsetenv\t\t GATKQUEUEDIR \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch \r\nsetenv\t\t GATKQUEUEEXAMPLES \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch\/resources \r\nsetenv\t\t GATKQUEUEBIN \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch\/bin \r\nsetenv\t\t GATKQUEUE_JAVA_MEM_MX 2g \r\nsetenv\t\t GATKQUEUE_JAVA_TMPDIR \/tmp \r\nsetenv\t\t GATKQUEUE_JAVA_OPTS -Xmx$GATKQUEUE_JAVA_MEM_MX -Djava.io.tmpdir=$GATKQUEUE_JAVA_TMPDIR \r\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/gatk+queue\/3.1.1\/noarch\/bin \r\n-------------------------------------------------------------------\r\n<\/pre>\n<pre>\r\n$ module whatis apps\/gatkqueue\/3.1.1\/noarch\r\napps\/gatkqueue\/3.1.1\/noarch: \r\n\r\n            Title: Genome Analysis Toolkit + Queue\r\n          Summary: Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines\r\n          License: Free for non-commercial use; registration required; see http:\/\/j.mp\/TTba2N\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/gatk\/index.php\r\n\r\n             Name: gatkqueue\r\n          Version: 3.1.1\r\n           Module: apps\/gatkqueue\/3.1.1\/noarch\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/gatkqueue\/3.1.1\/noarch\r\n     Package path: \/opt\/gridware\/pkg\/apps\/gatkqueue\/3.1.1\/noarch\r\n\r\n       Repository: file:\/opt\/gridware\/etc\/repos\/local\r\n          Package: ext\/gatk+queue\/3.x@05599477\r\n      Last update: 2014-04-14\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-04-14T10:58:34\r\n 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\r\n         Compiler: N\/A\r\n\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/gatkqueue\/3.1.1\/noarch\r\n<\/pre>\n<pre>\r\n$ module help apps\/gatkqueue\/3.1.1\/noarch\r\n\r\n----------- Module Specific Help for 'apps\/gatkqueue\/3.1.1\/noarch' ---------------------------\r\n\r\n\r\n          ======== Genome Analysis Toolkit + Queue ========          \r\n       Broad Institute package for analysing next-generation        \r\n        resequencing data; including command-line scripting         \r\n        framework for defining multi-stage genomic analysis         \r\n                              pipelines                              \r\n          ================================================          \r\n\r\nThis module sets up your environment for the use of the 'gatkqueue'\r\napplication. This module sets up version '3.1.1' of the\r\napplication.\r\n\r\n\r\n&gt;&gt; SYNOPSIS &lt;&gt; LICENSING &lt;&gt; FURTHER INFORMATION &lt;&gt; GET STARTED &lt;&lt;\r\n\r\nPlease refer to the website for further details on usage of this\r\npackage.\r\n<\/pre>\n<p>Lampredi HPC<br \/>\nigm-lampredi-users@ncl.ac.uk<\/p>\n<p>IGM IT<br \/>\nigmithelp@ncl.ac.uk<br \/>\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"<p>$ 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 <a href='https:\/\/blogs.ncl.ac.uk\/igmit\/?p=395' class='excerpt-more'>[&#8230;]<\/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],"class_list":["post-395","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","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\/395","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=395"}],"version-history":[{"count":1,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/395\/revisions"}],"predecessor-version":[{"id":396,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/395\/revisions\/396"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=395"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=395"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}