UCSC Executables

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.

Versions

• 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/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