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

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:

#!/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...

#!/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...

#!/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...

#!/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...

#!/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...