# HG changeset patch # User Jim Johnson # Date 1383769056 21600 # Node ID 822c8d19cfe383cac7d38d0c15792c4b9d8e0c5a # Parent b05b788e39891c8d00711b6956d43d4499f45e27 Download binary executables if avaiablable, otherwise compile from src diff -r b05b788e3989 -r 822c8d19cfe3 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 06 08:25:46 2013 -0400 +++ b/tool_dependencies.xml Wed Nov 06 14:17:36 2013 -0600 @@ -2,6 +2,469 @@ + + + + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/addCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ameme + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/autoDtd + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/autoSql + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/autoXml + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ave + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/aveCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/axtChain + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/axtSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/axtSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/axtToMaf + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/axtToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedCommonRegions + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedCoverage + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGeneParts + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedIntersect + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedItemOverlapCount + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedPileUps + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedRemoveOverlap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedRestrictToPositions + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToExons + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedWeedOverlapping + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedNamedItems + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedSummary + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigAverageOverBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigCorrelate + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigMerge + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blastToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blastXmlToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/calc + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/catDir + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/catUncomment + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainAntiRepeat + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainMergeSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainNet + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainPreNet + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainStitchId + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chainToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/checkAgpAndFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/checkCoverageGaps + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/checkHgFindSpec + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/checkTableCoords + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chopFaLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chromGraphFromBin + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/chromGraphToBin + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/colTransform + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/countChars + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/crTreeIndexBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/crTreeSearchBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/dbSnoop + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/dbTrash + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/estOrient + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCmp + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faFilterN + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faNoise + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faOneRecord + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faPolyASizes + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faRandomize + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faRc + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSize + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToFastq + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faTrans + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fastqToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/featureBits + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/findMotif + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gapToLift + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredHisto + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredSingleCover + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToFakePsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToMafFrames + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gmtime + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/headRest + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgFindSpec + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgGcPercent + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgLoadBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgLoadOut + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgLoadWiggle + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgTrackDb + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgWiggle + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgsql + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hgsqldump + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/htmlCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hubCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ixIxx + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/lavToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/lavToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ldHgGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOverMerge + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftUp + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/linesToRa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/localtime + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafAddIRows + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafAddQRows + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafCoverage + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafFetch + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafFrags + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafMeFirst + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafOrder + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafRanges + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafSpeciesList + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafSpeciesSubset + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafSplitPos + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mafsInRegion + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/makeTableList + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/maskOutFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mktime + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/mrnaToGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netChainSubset + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netClass + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netSyntenic + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/netToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/newProg + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/nibFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/nibSize + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/oligoMatch + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/overlapSelect + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/paraFetch + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/paraSync + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/positionalTblCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCat + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslDropOverlap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslHisto + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslLiftSubrangeBlat + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslMap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslMrnaCover + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslPairs + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslPartition + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslPretty + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslRecalcMatch + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslReps + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslSelect + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslStats + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslToChain + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslToPslx + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslxToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/qaToQac + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/qacAgpLift + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/qacToQa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/qacToWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/raSqlQuery + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/raToLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/raToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/randomLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/rmFaDups + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/rowsToCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/sizeof + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/spacedToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/splitFile + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/splitFileByColumn + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/sqlToXml + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/stringify + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/subChar + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/subColumn + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/tailLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/tdbQuery + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/textHistogram + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/tickToDate + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/toLower + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/toUpper + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/trfBig + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitDup + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitMask + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/validateFiles + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/validateManifest + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigCorrelate + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigEncode + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wordLine + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/xmlCat + ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/xmlToSql + + . + $INSTALL_DIR/bin + + + + + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/addCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ameme + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/autoDtd + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/autoSql + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/autoXml + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ave + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/aveCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/axtChain + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/axtSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/axtSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/axtToMaf + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/axtToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedClip + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedCommonRegions + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedCoverage + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedExtendRanges + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGeneParts + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedIntersect + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedItemOverlapCount + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedPileUps + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedRemoveOverlap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedRestrictToPositions + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedToBigBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedToExons + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedWeedOverlapping + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigBedInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigBedNamedItems + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigBedSummary + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigBedToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigAverageOverBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigCorrelate + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigMerge + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigSummary + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blastToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blastXmlToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/calc + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/catDir + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/catUncomment + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainAntiRepeat + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainMergeSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainNet + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainPreNet + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainStitchId + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chainToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/checkAgpAndFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/checkCoverageGaps + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/checkHgFindSpec + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/checkTableCoords + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chopFaLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chromGraphFromBin + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/chromGraphToBin + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/colTransform + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/countChars + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/crTreeIndexBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/crTreeSearchBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/dbSnoop + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/dbTrash + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/estOrient + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faCmp + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faCount + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faFilterN + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faNoise + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faOneRecord + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faPolyASizes + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faRandomize + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faRc + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faSize + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faSomeRecords + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToFastq + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faTrans + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/fastqToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/featureBits + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/fetchChromSizes + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/findMotif + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gapToLift + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredHisto + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredSingleCover + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredToFakePsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredToGtf + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/genePredToMafFrames + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfClient + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfServer + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gff3ToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gff3ToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gmtime + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gtfToGenePred + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/headRest + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgFindSpec + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgGcPercent + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgLoadBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgLoadOut + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgLoadWiggle + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgTrackDb + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgWiggle + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgsql + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hgsqldump + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/htmlCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/hubCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ixIxx + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/lavToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/lavToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ldHgGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOverMerge + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftUp + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/linesToRa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/localtime + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafAddIRows + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafAddQRows + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafCoverage + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafFetch + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafFrags + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafMeFirst + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafOrder + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafRanges + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafSpeciesList + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafSpeciesSubset + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafSplitPos + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafToPsl + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mafsInRegion + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/makeTableList + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/maskOutFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mktime + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/mrnaToGene + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netChainSubset + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netClass + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netSplit + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netSyntenic + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netToAxt + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/netToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/newProg + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/nibFrag + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/nibSize + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/oligoMatch + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/overlapSelect + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/paraFetch + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/paraSync + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/positionalTblCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslCDnaFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslCat + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslCheck + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslDropOverlap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslFilter + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslHisto + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslLiftSubrangeBlat + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslMap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslMrnaCover + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslPairs + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslPartition + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslPretty + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslRecalcMatch + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslReps + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslSelect + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslSort + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslStats + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslSwap + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslToBed + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslToChain + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslToPslx + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/pslxToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/qaToQac + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/qacAgpLift + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/qacToQa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/qacToWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/raSqlQuery + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/raToLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/raToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/randomLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/rmFaDups + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/rowsToCols + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/sizeof + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/spacedToTab + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/splitFile + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/splitFileByColumn + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/sqlToXml + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/stringify + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/subChar + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/subColumn + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/tailLines + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/tdbQuery + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/textHistogram + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/tickToDate + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/toLower + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/toUpper + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/trfBig + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/twoBitDup + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/twoBitInfo + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/twoBitMask + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/twoBitToFa + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/validateFiles + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/validateManifest + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/wigCorrelate + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/wigEncode + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/wigToBigWig + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/wordLine + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/xmlCat + ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/xmlToSql + chmod ugo+x * + + . + $INSTALL_DIR/bin + + + http://hgdownload.cse.ucsc.edu/admin/jksrc.zip @@ -14,16 +477,17 @@ cd ../gfServer; make; cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile; make - - $INSTALL_DIR/bin + + + $INSTALL_DIR/bin - + Downloads and installs the latest kent tools from UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip ( The website doesn't offer previously released versions.) -NOTE: This only handles blat for a NON-COMMERCIAL system. +NOTE: A license is required for use in a COMMERCIAL system. Blat source and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com/).