.. _backbone-label: Kentutils ============================== Introduction ~~~~~~~~ Kentutils: UCSC command line bioinformatic utilities. | For more information, please check: | Docker hub: https://hub.docker.com/r/genomicpariscentre/kentutils | Home page: https://github.com/ENCODE-DCC/kentUtils .. 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 - 302.1.0 * - BELL - 302.1.0 * - GAUTSCHI - 302.1.0 * - NEGISHI - 302.1.0 * - SCHOLAR - 302.1.0 Commands ~~~~~~~ - addCols - ameme - autoDtd - autoSql - autoXml - ave - aveCols - axtChain - axtSort - axtSwap - axtToMaf - axtToPsl - bedClip - bedCommonRegions - bedCoverage - bedExtendRanges - bedGeneParts - bedGraphPack - bedGraphToBigWig - bedIntersect - bedItemOverlapCount - bedPileUps - bedRemoveOverlap - bedRestrictToPositions - bedSort - bedToBigBed - bedToExons - bedToGenePred - bedToPsl - bedWeedOverlapping - bigBedInfo - bigBedNamedItems - bigBedSummary - bigBedToBed - bigWigAverageOverBed - bigWigCat - bigWigCorrelate - bigWigInfo - bigWigMerge - bigWigSummary - bigWigToBedGraph - bigWigToWig - blastToPsl - blastXmlToPsl - calc - catDir - catUncomment - chainAntiRepeat - chainFilter - chainMergeSort - chainNet - chainPreNet - chainSort - chainSplit - chainStitchId - chainSwap - chainToAxt - chainToPsl - checkAgpAndFa - checkCoverageGaps - checkHgFindSpec - checkTableCoords - chopFaLines - chromGraphFromBin - chromGraphToBin - colTransform - countChars - crTreeIndexBed - crTreeSearchBed - dbSnoop - dbTrash - estOrient - faCmp - faCount - faFilter - faFilterN - faFrag - faNoise - faOneRecord - faPolyASizes - faRandomize - faRc - faSize - faSomeRecords - faSplit - faToFastq - faToTab - faToTwoBit - faTrans - fastqToFa - featureBits - fetchChromSizes - findMotif - gapToLift - genePredCheck - genePredHisto - genePredSingleCover - genePredToBed - genePredToFakePsl - genePredToGtf - genePredToMafFrames - gfClient - gfServer - gff3ToGenePred - gff3ToPsl - gmtime - gtfToGenePred - headRest - hgFindSpec - hgGcPercent - hgLoadBed - hgLoadOut - hgLoadWiggle - hgTrackDb - hgWiggle - hgsql - hgsqldump - htmlCheck - hubCheck - ixIxx - lavToAxt - lavToPsl - ldHgGene - liftOver - liftOverMerge - liftUp - linesToRa - linux.x86_64 - localtime - mafAddIRows - mafAddQRows - mafCoverage - mafFetch - mafFilter - mafFrag - mafFrags - mafGene - mafMeFirst - mafOrder - mafRanges - mafSpeciesList - mafSpeciesSubset - mafSplit - mafSplitPos - mafToAxt - mafToPsl - mafsInRegion - makeTableList - maskOutFa - mktime - mrnaToGene - netChainSubset - netClass - netFilter - netSplit - netSyntenic - netToAxt - netToBed - newProg - nibFrag - nibSize - oligoMatch - overlapSelect - paraFetch - paraSync - positionalTblCheck - pslCDnaFilter - pslCat - pslCheck - pslDropOverlap - pslFilter - pslHisto - pslLiftSubrangeBlat - pslMap - pslMrnaCover - pslPairs - pslPartition - pslPretty - pslRecalcMatch - pslReps - pslSelect - pslSort - pslStats - pslSwap - pslToBed - pslToChain - pslToPslx - pslxToFa - qaToQac - qacAgpLift - qacToQa - qacToWig - raSqlQuery - raToLines - raToTab - randomLines - rmFaDups - rowsToCols - sizeof - spacedToTab - splitFile - splitFileByColumn - sqlToXml - stringify - subChar - subColumn - tailLines - tdbQuery - textHistogram - tickToDate - toLower - toUpper - trfBig - twoBitDup - twoBitInfo - twoBitMask - twoBitToFa - validateFiles - validateManifest - wigCorrelate - wigEncode - wigToBigWig - wordLine - xmlCat - xmlToSql Module ~~~~~~~~ You can load the modules by:: module load biocontainers module load kentutils 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 kentutils 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=kentutils #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers kentutils # Your kentutils 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=kentutils #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers kentutils # Your kentutils 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=kentutils #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers kentutils # Your kentutils 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=kentutils #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers kentutils # Your kentutils 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=kentutils #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers kentutils # Your kentutils workflow...