Software: UCSC Executables (ucsc_genome_toolkit)
Description
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.
Available Versions
| Unspecified: | 369 |
|---|
These executables have been downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ and made available on RCAC clusters.
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/369
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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