danielecook
2/17/2016 - 3:44 AM

Fetch ucsc tools and stash in homebrew directory.

Fetch ucsc tools and stash in homebrew directory.

get_ucsc_tool addCols 
get_ucsc_tool ameme 
get_ucsc_tool autoDtd 
get_ucsc_tool autoSql 
get_ucsc_tool autoXml 
get_ucsc_tool ave 
get_ucsc_tool aveCols 
get_ucsc_tool axtChain
get_ucsc_tool axtSort 
get_ucsc_tool axtSwap 
get_ucsc_tool axtToMaf
get_ucsc_tool axtToPsl
get_ucsc_tool bedClip 
get_ucsc_tool bedCommonRegions
get_ucsc_tool bedCoverage 
get_ucsc_tool bedExtendRanges 
get_ucsc_tool bedGeneParts
get_ucsc_tool bedGraphPack
get_ucsc_tool bedGraphToBigWig
get_ucsc_tool bedIntersect
get_ucsc_tool bedItemOverlapCount 
get_ucsc_tool bedPileUps
get_ucsc_tool bedRemoveOverlap
get_ucsc_tool bedRestrictToPositions
get_ucsc_tool bedSort 
get_ucsc_tool bedToBigBed 
get_ucsc_tool bedToExons
get_ucsc_tool bedToGenePred 
get_ucsc_tool bedToPsl
get_ucsc_tool bedWeedOverlapping
get_ucsc_tool bigBedInfo
get_ucsc_tool bigBedNamedItems
get_ucsc_tool bigBedSummary 
get_ucsc_tool bigBedToBed 
get_ucsc_tool bigPslToPsl 
get_ucsc_tool bigWigAverageOverBed
get_ucsc_tool bigWigCat 
get_ucsc_tool bigWigCluster 
get_ucsc_tool bigWigCorrelate 
get_ucsc_tool bigWigInfo
get_ucsc_tool bigWigMerge 
get_ucsc_tool bigWigSummary 
get_ucsc_tool bigWigToBedGraph
get_ucsc_tool bigWigToWig 
get_ucsc_tool blastToPsl
get_ucsc_tool blastXmlToPsl 
get_ucsc_tool blat
get_ucsc_tool calc
get_ucsc_tool catDir
get_ucsc_tool catUncomment
get_ucsc_tool chainAntiRepeat 
get_ucsc_tool chainFilter 
get_ucsc_tool chainMergeSort
get_ucsc_tool chainNet
get_ucsc_tool chainPreNet 
get_ucsc_tool chainSort 
get_ucsc_tool chainSplit
get_ucsc_tool chainStitchId 
get_ucsc_tool chainSwap 
get_ucsc_tool chainToAxt
get_ucsc_tool chainToPsl
get_ucsc_tool chainToPslBasic 
get_ucsc_tool checkAgpAndFa 
get_ucsc_tool checkCoverageGaps 
get_ucsc_tool checkHgFindSpec 
get_ucsc_tool checkTableCoords
get_ucsc_tool chopFaLines 
get_ucsc_tool chromGraphFromBin 
get_ucsc_tool chromGraphToBin 
get_ucsc_tool colTransform
get_ucsc_tool countChars
get_ucsc_tool crTreeIndexBed
get_ucsc_tool crTreeSearchBed 
get_ucsc_tool dbSnoop 
get_ucsc_tool dbTrash 
get_ucsc_tool estOrient 
get_ucsc_tool faAlign 
get_ucsc_tool faCmp 
get_ucsc_tool faCount 
get_ucsc_tool faFilter
get_ucsc_tool faFilterN 
get_ucsc_tool faFrag
get_ucsc_tool faNoise 
get_ucsc_tool faOneRecord 
get_ucsc_tool faPolyASizes
get_ucsc_tool faRandomize 
get_ucsc_tool faRc
get_ucsc_tool faSize
get_ucsc_tool faSomeRecords 
get_ucsc_tool faSplit 
get_ucsc_tool faToFastq 
get_ucsc_tool faToTab 
get_ucsc_tool faToTwoBit
get_ucsc_tool faTrans 
get_ucsc_tool fastqToFa 
get_ucsc_tool featureBits 
get_ucsc_tool fetchChromSizes 
get_ucsc_tool findMotif 
get_ucsc_tool gapToLift 
get_ucsc_tool genePredCheck 
get_ucsc_tool genePredFilter
get_ucsc_tool genePredHisto 
get_ucsc_tool genePredSingleCover 
get_ucsc_tool genePredToBed 
get_ucsc_tool genePredToBigGenePred 
get_ucsc_tool genePredToFakePsl 
get_ucsc_tool genePredToGtf 
get_ucsc_tool genePredToMafFrames 
get_ucsc_tool getRna
get_ucsc_tool getRnaPred
get_ucsc_tool gff3ToGenePred
get_ucsc_tool gff3ToPsl 
get_ucsc_tool gmtime
get_ucsc_tool gtfToGenePred 
get_ucsc_tool headRest
get_ucsc_tool hgFindSpec
get_ucsc_tool hgGcPercent 
get_ucsc_tool hgLoadBed 
get_ucsc_tool hgLoadChain 
get_ucsc_tool hgLoadMaf 
get_ucsc_tool hgLoadMafSummary
get_ucsc_tool hgLoadNet 
get_ucsc_tool hgLoadOut 
get_ucsc_tool hgLoadOutJoined 
get_ucsc_tool hgLoadWiggle
get_ucsc_tool hgSpeciesRna
get_ucsc_tool hgTrackDb 
get_ucsc_tool hgWiggle
get_ucsc_tool hgsql 
get_ucsc_tool hgsqldump 
get_ucsc_tool htmlCheck 
get_ucsc_tool hubCheck
get_ucsc_tool hubPublicCheck
get_ucsc_tool ixIxx 
get_ucsc_tool lavToAxt
get_ucsc_tool lavToPsl
get_ucsc_tool ldHgGene
get_ucsc_tool liftOver
get_ucsc_tool liftOverMerge 
get_ucsc_tool liftUp
get_ucsc_tool linesToRa 
get_ucsc_tool localtime 
get_ucsc_tool mafAddIRows 
get_ucsc_tool mafAddQRows 
get_ucsc_tool mafCoverage 
get_ucsc_tool mafFetch
get_ucsc_tool mafFilter 
get_ucsc_tool mafFrag 
get_ucsc_tool mafFrags
get_ucsc_tool mafGene 
get_ucsc_tool mafMeFirst
get_ucsc_tool mafOrder
get_ucsc_tool mafRanges 
get_ucsc_tool mafSpeciesList
get_ucsc_tool mafSpeciesSubset
get_ucsc_tool mafSplit
get_ucsc_tool mafSplitPos 
get_ucsc_tool mafToAxt
get_ucsc_tool mafToPsl
get_ucsc_tool mafToSnpBed 
get_ucsc_tool mafsInRegion
get_ucsc_tool makeTableList 
get_ucsc_tool maskOutFa 
get_ucsc_tool mktime
get_ucsc_tool mrnaToGene
get_ucsc_tool netChainSubset
get_ucsc_tool netClass
get_ucsc_tool netFilter 
get_ucsc_tool netSplit
get_ucsc_tool netSyntenic 
get_ucsc_tool netToAxt
get_ucsc_tool netToBed
get_ucsc_tool newProg 
get_ucsc_tool newPythonProg 
get_ucsc_tool nibFrag 
get_ucsc_tool nibSize 
get_ucsc_tool oligoMatch
get_ucsc_tool overlapSelect 
get_ucsc_tool paraFetch 
get_ucsc_tool paraSync
get_ucsc_tool positionalTblCheck
get_ucsc_tool pslCDnaFilter 
get_ucsc_tool pslCat
get_ucsc_tool pslCheck
get_ucsc_tool pslDropOverlap
get_ucsc_tool pslFilter 
get_ucsc_tool pslHisto
get_ucsc_tool pslLiftSubrangeBlat 
get_ucsc_tool pslMap
get_ucsc_tool pslMrnaCover
get_ucsc_tool pslPairs
get_ucsc_tool pslPartition
get_ucsc_tool pslPosTarget
get_ucsc_tool pslPretty 
get_ucsc_tool pslRecalcMatch
get_ucsc_tool pslReps 
get_ucsc_tool pslScore
get_ucsc_tool pslSelect 
get_ucsc_tool pslSort 
get_ucsc_tool pslStats
get_ucsc_tool pslSwap 
get_ucsc_tool pslToBed
get_ucsc_tool pslToBigPsl 
get_ucsc_tool pslToChain
get_ucsc_tool pslToPslx 
get_ucsc_tool pslxToFa
get_ucsc_tool qaToQac 
get_ucsc_tool qacAgpLift
get_ucsc_tool qacToQa 
get_ucsc_tool qacToWig
get_ucsc_tool raSqlQuery
get_ucsc_tool raToLines 
get_ucsc_tool raToTab 
get_ucsc_tool randomLines 
get_ucsc_tool rmFaDups
get_ucsc_tool rowsToCols
get_ucsc_tool sizeof
get_ucsc_tool spacedToTab 
get_ucsc_tool splitFile 
get_ucsc_tool splitFileByColumn 
get_ucsc_tool sqlToXml
get_ucsc_tool stringify 
get_ucsc_tool subChar 
get_ucsc_tool subColumn 
get_ucsc_tool tailLines 
get_ucsc_tool tdbQuery
get_ucsc_tool textHistogram 
get_ucsc_tool tickToDate
get_ucsc_tool toLower 
get_ucsc_tool toUpper 
get_ucsc_tool transMapPslToGenePred 
get_ucsc_tool trfBig
get_ucsc_tool twoBitDup 
get_ucsc_tool twoBitInfo
get_ucsc_tool twoBitMask
get_ucsc_tool twoBitToFa
get_ucsc_tool validateFiles 
get_ucsc_tool validateManifest
get_ucsc_tool wigCorrelate
get_ucsc_tool wigEncode 
get_ucsc_tool wigToBigWig 
get_ucsc_tool wordLine
get_ucsc_tool xmlCat
get_ucsc_tool xmlToSql 
function get_ucsc_tool() {
    curl http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/${1} > `brew --prefix`/bin/${1}
    chmod +x `brew --prefix`/bin/${1}
}