Introduction ~~~~~~~ UCSC Executables
is 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.
These executables have been downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ and made available on RCAC clusters.
- 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
You can load the modules by:
module load biocontainers
module load ucsc_genome_toolkit/369
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 executables on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=UCSC
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ucsc_genome_toolkit/369
blat genome.fasta input.fasta blat.out
fastqToFa input.fastq output.fasta