.. _backbone-label: Ucsc_genome_toolkit ============================== Introduction ~~~~~~~~ UCSC genome toolkit is a collection of a variety of executables that perform functions ranging from sequence analysis and format conversion, to basic number crunching and statistics, to complex database generation and manipulation. | For more information, please check: | Docker hub: https://hub.docker.com/r/rahulg603/ucsc_genome_toolkit | Home page: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64.v369/ .. note:: Please follow the recommended citation guidelines from the developers when you use the tool in research. Versions ~~~~~~~ .. list-table:: :width: 100 % :widths: 25 75 :header-rows: 1 * - Cluster - Version(s) * - ANVIL - 369 * - BELL - 369 * - GAUTSCHI - 369 * - NEGISHI - 369 * - SCHOLAR - 369 Commands ~~~~~~~ - addCols - ameme - autoDtd - autoSql - autoXml - ave - aveCols - axtChain - axtSort - axtSwap - axtToMaf - axtToPsl - bamToPsl - barChartMaxLimit - bedClip - bedCommonRegions - bedCoverage - bedExtendRanges - bedGeneParts - bedGraphPack - bedGraphToBigWig - bedIntersect - bedItemOverlapCount - bedJoinTabOffset - bedJoinTabOffset.py - bedMergeAdjacent - bedPartition - bedPileUps - bedRemoveOverlap - bedRestrictToPositions - bedSingleCover.pl - bedSort - bedToBigBed - bedToExons - bedToGenePred - bedToPsl - bedWeedOverlapping - bigBedInfo - bigBedNamedItems - bigBedSummary - bigBedToBed - bigGenePredToGenePred - bigHeat - bigMafToMaf - bigPslToPsl - bigWigAverageOverBed - bigWigCat - bigWigCluster - bigWigCorrelate - bigWigInfo - bigWigMerge - bigWigSummary - bigWigToBedGraph - bigWigToWig - binFromRange - blastToPsl - blastXmlToPsl - blat - calc - catDir - catUncomment - chainAntiRepeat - chainBridge - chainCleaner - chainFilter - chainMergeSort - chainNet - chainPreNet - chainScore - chainSort - chainSplit - chainStitchId - chainSwap - chainToAxt - chainToPsl - chainToPslBasic - checkAgpAndFa - checkCoverageGaps - checkHgFindSpec - checkTableCoords - chopFaLines - chromGraphFromBin - chromGraphToBin - chromToUcsc - clusterGenes - clusterMatrixToBarChartBed - colTransform - countChars - cpg_lh - crTreeIndexBed - crTreeSearchBed - dbSnoop - dbTrash - endsInLf - estOrient - expMatrixToBarchartBed - faAlign - faCmp - faCount - faFilter - faFilterN - faFrag - faNoise - faOneRecord - faPolyASizes - faRandomize - faRc - faSize - faSomeRecords - faSplit - faToFastq - faToTab - faToTwoBit - faToVcf - faTrans - fastqStatsAndSubsample - fastqToFa - featureBits - fetchChromSizes - findMotif - fixStepToBedGraph.pl - gapToLift - genePredCheck - genePredFilter - genePredHisto - genePredSingleCover - genePredToBed - genePredToBigGenePred - genePredToFakePsl - genePredToGtf - genePredToMafFrames - genePredToProt - gensub2 - getRna - getRnaPred - gff3ToGenePred - gff3ToPsl - gmtime - gtfToGenePred - headRest - hgBbiDbLink - hgFakeAgp - hgFindSpec - hgGcPercent - hgGoldGapGl - hgLoadBed - hgLoadChain - hgLoadGap - hgLoadMaf - hgLoadMafSummary - hgLoadNet - hgLoadOut - hgLoadOutJoined - hgLoadSqlTab - hgLoadWiggle - hgSpeciesRna - hgTrackDb - hgWiggle - hgsql - hgsqldump - hgvsToVcf - hicInfo - htmlCheck - hubCheck - hubClone - hubPublicCheck - ixIxx - lastz-1.04.00 - lastz_D-1.04.00 - lavToAxt - lavToPsl - ldHgGene - liftOver - liftOverMerge - liftUp - linesToRa - localtime - mafAddIRows - mafAddQRows - mafCoverage - mafFetch - mafFilter - mafFrag - mafFrags - mafGene - mafMeFirst - mafNoAlign - mafOrder - mafRanges - mafSpeciesList - mafSpeciesSubset - mafSplit - mafSplitPos - mafToAxt - mafToBigMaf - mafToPsl - mafToSnpBed - mafsInRegion - makeTableList - maskOutFa - matrixClusterColumns - matrixMarketToTsv - matrixNormalize - mktime - mrnaToGene - netChainSubset - netClass - netFilter - netSplit - netSyntenic - netToAxt - netToBed - newProg - newPythonProg - nibFrag - nibSize - oligoMatch - overlapSelect - para - paraFetch - paraHub - paraHubStop - paraNode - paraNodeStart - paraNodeStatus - paraNodeStop - paraSync - paraTestJob - parasol - positionalTblCheck - pslCDnaFilter - pslCat - pslCheck - pslDropOverlap - pslFilter - pslHisto - pslLiftSubrangeBlat - pslMap - pslMapPostChain - pslMrnaCover - pslPairs - pslPartition - pslPosTarget - pslPretty - pslRc - pslRecalcMatch - pslRemoveFrameShifts - pslReps - pslScore - pslSelect - pslSomeRecords - pslSort - pslSortAcc - pslStats - pslSwap - pslToBed - pslToBigPsl - pslToChain - pslToPslx - pslxToFa - qaToQac - qacAgpLift - qacToQa - qacToWig - raSqlQuery - raToLines - raToTab - randomLines - rmFaDups - rowsToCols - sizeof - spacedToTab - splitFile - splitFileByColumn - sqlToXml - strexCalc - stringify - subChar - subColumn - tabQuery - tailLines - tdbQuery - tdbRename - tdbSort - textHistogram - tickToDate - toLower - toUpper - trackDbIndexBb - transMapPslToGenePred - trfBig - twoBitDup - twoBitInfo - twoBitMask - twoBitToFa - ucscApiClient - udr - vai.pl - validateFiles - validateManifest - varStepToBedGraph.pl - webSync - wigCorrelate - wigEncode - wigToBigWig - wordLine - xmlCat - xmlToSql Module ~~~~~~~~ You can load the modules by:: module load biocontainers module load ucsc_genome_toolkit Example job ~~~~~ .. warning:: Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead. To run ucsc_genome_toolkit on our clusters: .. tab-set:: .. tab-item:: Anvil .. code-block:: bash #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -p wholenode # Partition name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=ucsc_genome_toolkit #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers ucsc_genome_toolkit # Your ucsc_genome_toolkit workflow... .. tab-item:: Bell, Gautschi, or Negishi .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p cpu # Partition name #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=ucsc_genome_toolkit #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers ucsc_genome_toolkit # Your ucsc_genome_toolkit workflow... .. tab-item:: Gautschi-AI .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p ai # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=ucsc_genome_toolkit #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers ucsc_genome_toolkit # Your ucsc_genome_toolkit workflow... .. tab-item:: Gilbreth .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p a100 # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH --mem=2G # Memory #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=ucsc_genome_toolkit #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers ucsc_genome_toolkit # Your ucsc_genome_toolkit workflow... .. tab-item:: Scholar .. code-block:: bash #!/bin/bash #SBATCH -A queue # Queue name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=ucsc_genome_toolkit #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers ucsc_genome_toolkit # Your ucsc_genome_toolkit workflow...