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