The UCSC Genome Browser is maintained using 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 compiled and made available on the Helix Systems.
The easiest way is to load the ucsc environment module:
$ module load ucsc
The module load statement can be placed in your startup files for permanency.
Then, just call the executable of choice on the commandline:
$ faSplit byname scaffolds.fa outRoot/
aarToAxt addAveMedScoreToPsls addCols affyPairsToSample agpAllToFaFile agpCloneCheck agpCloneList agpMergeChromScaf agpToFa agpToGl agxToBed agxToIntronBeds agxToTxg allenCollectSeq altAnalysis altPaths altSplice altSummary aNotB apacheMonitor assessLibs autoDtd autoSql autoXml ave aveCols averagExp averageZoomLevels avgTranscriptomeExps axtAndBed axtBest axtCalcMatrix axtChain axtDropOverlap axtDropSelf axtFilter axtForEst axtIndex axtPretty axtQueryCount axtRecipBest axtRescore axtSort axtSplitByTarget axtSwap axtToBed axtToChain axtToMaf axtToPsl bamToPsl barChartMaxLimit bedClip bedCommonRegions bedCons bedCoverage bedDown bedExtendRanges bedGeneParts bedGraphPack bedGraphToBigWig bedInGraph bedIntersect bedItemOverlapCount bedJoinTabOffset bedJoinTabOffset.py bedMergeAdjacent bedOrBlocks bedPartition bedPileUps bedRemoveOverlap bedRestrictToPositions bedSort bedSplitOnChrom bedToBigBed bedToExons bedToFrames bedToGenePred bedToPsl bedToTxEdges bedUp bedWeedOverlapping bigBedInfo bigBedNamedItems bigBedSummary bigBedToBed bigChainBreaks bigGenePredToGenePred bigGuessDb bigHeat bigMafToMaf bigPslToPsl bigWigAverageOverBed bigWigCat bigWigCluster bigWigCorrelate bigWigInfo bigWigMerge bigWigSummary bigWigToBedGraph bigWigToWig binFromRange blastToPsl blastXmlToPsl blat blatServersCheck blatz blatzClient blatzServer borfBig buildReleaseLog calc calcGap catDir catUncomment ccCp chainAntiRepeat chainBridge chainCleaner chainDbToFile chainFilter chainMergeSort chainNet chainPreNet chainScore chainSort chainSplit chainStitchId chainSwap chainToAxt chainToPsl chainToPslBasic checkableBorf checkAgpAndFa checkBigDbSnp checkCardinality checkChain checkCoverageGaps checkHgFindSpec checkSgdSync checkTableCoords checkUrlsInTable chopFaLines chromGraphFromBin chromGraphToBin chromToUcsc clusterGenes clusterMatrixToBarChartBed clusterPsl clusterRna colTransform consForBed convolve countChars countNib cpg_lh createSageSummary crTreeIndexBed crTreeSearchBed ctgFaToFa ctgToChromFa dbDbToHubTxt dbFindFieldsWith dbSnoop dbSnpJsonToTab dbTrash detab dnaMotifFind dnsInfo dumpNib edwAddAssembly edwAddQaContamTarget edwAddQaEnrichTarget edwAddSubscriber edwChangeFormat edwComparePeaks edwCorrectFileTags edwCreateUser edwFakeManifestFromSubmit edwJob edwMakeContaminationQa edwMakeEnrichments edwMakePairedEndQa edwMakeRepeatQa edwMakeReplicateQa edwMakeValidFile edwQaEvaluate edwReallyRemoveFiles edwReplicatedPeaks edwRetryJob edwRsyncEdwUser edwRunDaemon edwRunOnIds edwSamPairedEndStats edwSolexaToSangerFastq edwSubmit eisenInput emblMatrixToMotif embossToPsl endsInLf estLibStats estOrient exonerateGffDoctor expMatrixToBarchartBed expToRna faAlign faCmp faCount faFilter faFilterN faFlyBaseToUcsc faFrag faGapLocs faGapSizes fakeFinContigs fakeOut faNcbiToUcsc faNoise faOneRecord faPolyASizes faRandomize faRc faRenameRecords faSimplify faSize faSomeRecords faSplit fastqStatsAndSubsample fastqToFa faToFastq faToNib faToTab faToTwoBit faToVcf faTrans faTrimPolyA faTrimRead featureBits fetchChromSizes ffaToFa findMotif findStanAlignments fishClones fixCr fixHarbisonMotifs fixStepToBedGraph.pl fqToQa fqToQac fragPart gapSplit gapToLift gbGetEntries gbOneAcc gbSeqCheck gbToFaRa gcForBed gencodeVersionForGenes genePredCheck genePredFilter genePredHisto genePredSingleCover genePredToBed genePredToBigGenePred genePredToFakePsl genePredToGtf genePredToMafFrames genePredToProt genePredToPsl geoMirrorNode getChroms getFeatDna getRna getRnaPred gfClient gff3ToGenePred gff3ToPsl gffPeek gfPcr gfServer git-reports gmtime gpcrParser gpStats gpToGtf groupSamples gsBig gtfToGenePred hapmapPhaseIIISummary headRest hgAddLiftOverChain hgAvidShortBed hgBbiDbLink hgBioCyc hgCeOrfToGene hgCGAP hgChroms hgClonePos hgClusterGenes hgCountAlign hgCtgPos hgDeleteChrom hgDropSplitTable hgEmblProtLinks hgExonerate hgExperiment hgExtFileCheck hgFakeAgp hgFiberglass hgFindSpec hgFlyBase hgGcPercent hgGeneBands hgGenericMicroarray hgGetAnn hgGnfMicroarray hgGoAssociation hgGoldGapGl hgGtex hgGtexAse hgGtexExonBed hgGtexGeneBed hgJaxQtl hgKegg hgKegg2 hgKegg3 hgKgGetText hgKgMrna hgKnownGeneList hgKnownMore hgKnownToSuper hgLoadBed hgLoadBlastTab hgLoadChain hgLoadChromGraph hgLoadEranModules hgLoadGap hgLoadGenePred hgLoadItemAttr hgLoadMaf hgLoadMafFrames hgLoadMafSummary hgLoadNet hgLoadNetDist hgLoadOut hgLoadOutJoined hgLoadPsl hgLoadRnaFold hgLoadSample hgLoadSeq hgLoadSqlTab hgLoadWiggle hgLsSnpPdbLoad hgMapMicroarray hgMapToGene hgMapViaSwissProt hgMaxExp hgMedianMicroarray hgMrnaRefseq hgNearTest hgNetDist hgNibSeq hgPar hgPepPred hgPhMouse hgProtIdToGenePred hgRatioMicroarray hgRenameSplitTable hgRnaGenes hgSanger20 hgSanger22 hgSelect hgSgdGff3 hgSgdGfp hgSgdPep hgSoftberryHom hgSoftPromoter hgSpeciesRna hgsql hgsqladmin hgsqldump hgsqlimport hgsqlSwapTables hgsqlTableDate hgStanfordMicroarray hgStsAlias hgStsMarkers hgSuperfam hgTablesTest hgTomRough hgTpf hgTraceInfo hgTrackDb hgTracksRandom hgvsToVcf hgWaba hgWiggle hgWormLinks hgYeastRegCode hicInfo hprdP2p htmlCheck htmlPics hubCheck hubClone hubCrawl hubPublicCheck intronEnds iriToControlTable iriToDnaMotif isPcr jkUniq joinableFields joinerCheck joinerRoute knownToHprd knownToVisiGene knownVsBlat kvsSummary lavToAxt lavToPsl ldHgGene lfsOverlap libScan liftAcross liftAgp liftFrags liftOver liftOverMerge liftPromoHits liftUp lineCount linesToRa localtime mafAddIRows mafAddQRows mafCoverage mafFetch mafFilter mafFrag mafFrags mafGene mafMeFirst mafNoAlign mafOrder mafRanges mafsInRegion mafSpeciesList mafSpeciesSubset mafSplit mafSplitPos mafToAxt mafToBigMaf mafToPsl mafToSnpBed makeTableDescriptions makeTableList makeTrackIndex maskOutFa matrixClusterColumns matrixMarketToTsv matrixNormalize matrixToBarChartBed maxTranscriptomeExps mdbPrint mdbUpdate mdToNcbiLift mgcFastaForBed mktime motifLogo motifSig mousePoster mrnaToGene mysqlSecurityCheck netChainSubset netClass netFilter netSplit netStats netSyntenic netToAxt netToBed netToBedWithId newProg newPythonProg nibbImageProbes nibbNameFix nibbParseImageDir nibbPrepImages nibFrag nibSize normalizeSampleFile nt4Frag oligoMatch orf orfStats orthoEvaluate orthologBySynteny orthoMap orthoPickIntron orthoSplice overlapSelect paraFetch paraSync patCount pepPredToFa phToPsl phyloRenameAndPrune polyInfo positionalTblCheck promoSeqFromCluster pslCat pslCDnaFilter pslCheck pslCoverage pslDiff pslDropOverlap pslFilter pslFilterPrimers pslFixCdsJoinGap pslGlue pslHisto pslHitPercent pslIntronsOnly pslLiftSubrangeBlat pslMap pslMapPostChain pslMismatchGapToBed pslMrnaCover pslPairs pslPartition pslPosTarget pslPretty pslProtToRnaCoords pslQuickFilter pslRc pslRecalcMatch pslRemoveFrameShifts pslReps pslScore pslSelect pslSimp pslSomeRecords pslSort pslSortAcc pslSplitOnTarget pslStats pslSwap pslToBed pslToBigPsl pslToChain pslToPslx pslToXa pslUniq pslUnpile pslxToFa qacAgpLift qacToQa qacToWig qaToQac randomLines raSqlQuery raToCds raToLines raToTab refreshNamedSessionCustomTrac refSeqGet regionPicker relPairs reviewIndexes rikenBestInCluster rmFaDups rmskAlignToPsl rnaFoldBig rowsToCols safePush samHit sanger22gtf scaffoldFaToAgp scaleSampleFiles scanRa scrambleFa semiNorm seqCheck sequenceForBed sim4big simpleChain sizeof snpException snpMaskAddInsertions snpMaskCutDeletions snpMaskSingle snpNcbiToUcsc snpValid spacedToTab spideyToPsl splitFa splitFaIntoContigs splitFile splitFileByColumn splitSim sqlToXml stageMultiz stanToBedAndExpRecs strexCalc stringify subChar subColumn subs subsetAxt subsetTraces tableSum tailLines tdbQuery tdbRename tdbSort testSearch textHist2 textHistogram tfbsConsLoc tfbsConsSort tickToDate timePosTable toDev64 toLower toUpper trackDbIndexBb trackDbPatch trackDbRaFormat trackDbToTxt trackOverlap transMapPslToGenePred trfBig twinOrf twinOrf2 twinOrf3 twinOrfStats twinOrfStats2 twinOrfStats3 twoBitDup twoBitInfo twoBitMask twoBitToFa txAbFragFind txBedToGraph txCdsBadBed txCdsCluster txCdsEvFromBed txCdsEvFromBorf txCdsEvFromProtein txCdsEvFromRna txCdsGoodBed txCdsOrfInfo txCdsOrtho txCdsPick txCdsPredict txCdsRaExceptions txCdsRefBestEvOnly txCdsRepick txCdsSuspect txCdsSvmInput txCdsToGene txCdsWeed txgAddEvidence txgAnalyze txGeneAccession txGeneAlias txGeneAltProt txGeneCanonical txGeneCdsMap txGeneColor txGeneExplainUpdate1 txGeneFromBed txGeneProtAndRna txGeneSeparateNoncoding txGeneXref txgGoodEdges txgToAgx txgToXml txgTrim txInfoAssemble txOrtho txPslFilter txPslToBed txReadRa txWalk ucscApiClient udcCleanup undupFa uniqSize updateStsInfo upper utrFa validateFiles validateManifest varStepToBedGraph.pl vcfFilter vcfRenameAndPrune vcfToBed vcfToHgvs vegaBuildInfo venn verticalSplitSqlTable webSync weedLines whyConserved wigBedToStep wigCorrelate wigEncode wigToBigWig wordLine xmlCat xmlToSql
For most of the executables, issuing the command without any arguments will give a brief description of the executable.
For example:
$ twoBitToFa
twoBitToFa - Convert all or part of .2bit file to fasta
usage:
twoBitToFa input.2bit output.fa
options:
-seq=name - restrict this to just one sequence
-start=X - start at given position in sequence (zero-based)
-end=X - end at given position in sequence (non-inclusive)
-seqList=file - file containing list of the desired sequence names
in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
where coordinates are half-open zero-based, i.e. [start,end)
-noMask - convert sequence to all upper case
-bpt=index.bpt - use bpt index instead of built in one
-bed=input.bed - grab sequences specified by input.bed. Will exclude introns
-bedPos - with -bed, to use chrom:start-end as the fasta ID in output.fa
Sequence and range may also be specified as part of the input
file name using the syntax:
/path/input.2bit:name
or
/path/input.2bit:name
or
/path/input.2bit:name:start-end
Many of the executables are poorly documented. For further help, you can submit questions to the main UCSC discussion list. See http://genome.ucsc.edu/contacts.html.