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

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:

#!/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...

#!/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...

#!/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...

#!/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...

#!/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...