docker build -t kenttools:0.1-1 -f dockerFile.txt . > docker.build.log 2>&1
The output of the docker build must be captured in a file via the redirect, otherwise unusual character sets displayed during the build can kill your terminal.
A sample set of kent commands have been include in this image. For example: featureBits, hgsql, twoBitInfo, faToTwoBit, twoBitToFa and the big* tools.
In the container:
$ ls /usr/local/bin
bigBedInfo bigWigAverageOverBed bigWigMerge featureBits
bigBedNamedItems bigWigCat bigWigSummary hgsql
bigBedSummary bigWigCluster bigWigToBedGraph twoBitInfo
bigBedToBed bigWigCorrelate bigWigToWig twoBitToFa
bigPslToPsl bigWigInfo faToTwoBit
There is a short test script in the ubuntu user home directory: testCommands.sh that will exercise a couple of these commands:
$ cat testCommands.sh
#!/bin/sh
printf "featureBits hg38 -countGaps knownGene\n" 1>&2
featureBits hg38 -countGaps knownGene > fb.hg38.knownGene.txt 2>&1
printf "hgsql -e 'desc trackVersion;' hgFixed\n" 1>&2
hgsql -e 'desc trackVersion;' hgFixed > trackVersion.hgFixed.txt
printf "bigBedInfo http://hgdownload.cse.ucsc.edu/gbdb/hg38/bbi/lrgRegions/lrg.bb\n" 1>&2
bigBedInfo http://hgdownload.cse.ucsc.edu/gbdb/hg38/bbi/lrgRegions/lrg.bb > lrg.bigBedInfo.txt
printf "bigWigInfo http://hgdownload.cse.ucsc.edu/gbdb/rn6/bbi/gc5BaseBw/gc5Base.bw\n" 1>&2
bigWigInfo http://hgdownload.cse.ucsc.edu/gbdb/rn6/bbi/gc5BaseBw/gc5Base.bw > gc5Base.bigWigInfo.txt
printf "twoBitInfo http://hgdownload.cse.ucsc.edu/gbdb/hg38/hg38.2bit stdout | sort -k2nr\n" 1>&2
twoBitInfo http://hgdownload.cse.ucsc.edu/gbdb/hg38/hg38.2bit stdout | sort -k2nr > hg38.chromSizes.txt
axtToMaf chainToPsl gff3ToGenePred mafsInRegion raSqlQuery
axtToPsl chainToPslBasic gff3ToPsl makeTableList raToLines
bedClip checkAgpAndFa gmtime maskOutFa raToTab
bedCommonRegions checkCoverageGaps gtfToGenePred mktime randomLines
bedCoverage checkHgFindSpec headRest mrnaToGene rmFaDups
bedExtendRanges checkTableCoords hgFindSpec netChainSubset rowsToCols
bedGeneParts chopFaLines hgGcPercent netClass sizeof
bedGraphPack chromGraphFromBin hgLoadBed netFilter spacedToTab
bedGraphToBigWig chromGraphToBin hgLoadChain netSplit splitFile
bedIntersect colTransform hgLoadMaf netSyntenic splitFileByColumn
bedItemOverlapCount countChars hgLoadMafSummary netToAxt sqlToXml
bedPileUps crTreeIndexBed hgLoadNet netToBed stringify
bedRemoveOverlap crTreeSearchBed hgLoadOut newProg subChar
bedRestrictToPositions dbSnoop hgLoadOutJoined newPythonProg subColumn
bedSort dbTrash hgLoadWiggle nibFrag tailLines
bedToBigBed estOrient hgSpeciesRna nibSize tdbQuery
bedToExons faAlign hgTrackDb oligoMatch textHistogram
bedToGenePred faCmp hgWiggle overlapSelect tickToDate
bedToPsl faCount hgsql paraFetch toLower
bedWeedOverlapping faFilter hgsqldump paraSync toUpper
bigBedInfo faFilterN htmlCheck positionalTblCheck transMapPslToGenePred
bigBedNamedItems faFrag hubCheck pslCDnaFilter trfBig
bigBedSummary faNoise hubPublicCheck pslCat twoBitDup
bigBedToBed faOneRecord ixIxx pslCheck twoBitInfo
bigPslToPsl faPolyASizes lavToAxt pslDropOverlap twoBitMask
bigWigAverageOverBed faRandomize lavToPsl pslFilter twoBitToFa
bigWigCat faRc ldHgGene pslHisto udr
bigWigCluster faSize liftOver pslLiftSubrangeBlat validateFiles
bigWigCorrelate faSomeRecords liftOverMerge pslMap validateManifest
bigWigInfo faSplit liftUp pslMrnaCover wigCorrelate
bigWigMerge faToFastq linesToRa pslPairs wigEncode
bigWigSummary faToTab localtime pslPartition wigToBigWig
bigWigToBedGraph faToTwoBit mafAddIRows pslPosTarget wordLine
bigWigToWig faTrans mafAddQRows pslPretty xmlCat
blastToPsl fastqToFa mafCoverage pslRecalcMatch xmlToSql
blastXmlToPsl featureBits mafFetch pslReps
fetchChromSizes mafFilter pslScore
calc findMotif mafFrag pslSelect
Of course, some of those may require additional linux packages to be installed in the container.