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donovan-h-parks

Allow CheckM data path to be set through the environmental variable C…

Apr 9, 2022

2c27394 · Apr 9, 2022

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Name		Name	Last commit message	Last commit date
parent directory ..
deprecated		deprecated	Why did Mike delete all my scripts?	Jul 20, 2014
genometreeworkflow		genometreeworkflow	Allow CheckM data path to be set through the environmental variable C…	Apr 9, 2022
__init__.py		__init__.py	Allow CheckM data path to be set through the environmental variable C…	Apr 9, 2022
calculateBounds.py		calculateBounds.py	Why did Mike delete all my scripts?	Jul 20, 2014
calculateBoundsTD.py		calculateBoundsTD.py	Why did Mike delete all my scripts?	Jul 20, 2014
calculateConservativeMarkerGenes.py		calculateConservativeMarkerGenes.py	Why did Mike delete all my scripts?	Jul 20, 2014
classTree.py		classTree.py	Why did Mike delete all my scripts?	Jul 20, 2014
classTreeInternalNodeMetadata.py		classTreeInternalNodeMetadata.py	Why did Mike delete all my scripts?	Jul 20, 2014
createMarketSetPlots.py		createMarketSetPlots.py	Why did Mike delete all my scripts?	Jul 20, 2014
createSelectedMarkerSetMapping.py		createSelectedMarkerSetMapping.py	Move to version 0.9.0.	Sep 4, 2014
createTaxonomicSpecificMarkerSets.py		createTaxonomicSpecificMarkerSets.py	Why did Mike delete all my scripts?	Jul 20, 2014
distributionDeltaCodingDensity.py		distributionDeltaCodingDensity.py	Why did Mike delete all my scripts?	Jul 20, 2014
distributionDeltaGC.py		distributionDeltaGC.py	Why did Mike delete all my scripts?	Jul 20, 2014
distributionDeltaTetraDiff.py		distributionDeltaTetraDiff.py	Why did Mike delete all my scripts?	Jul 20, 2014
evaluatePfamTigrfamHMMs.py		evaluatePfamTigrfamHMMs.py	Why did Mike delete all my scripts?	Jul 20, 2014
evaluateProdigal.py		evaluateProdigal.py	Why did Mike delete all my scripts?	Jul 20, 2014
findCircularSeqs.py		findCircularSeqs.py	Why did Mike delete all my scripts?	Jul 20, 2014
geneCountDict.py		geneCountDict.py	Why did Mike delete all my scripts?	Jul 20, 2014
genomeCharacteristics.py		genomeCharacteristics.py	Why did Mike delete all my scripts?	Jul 20, 2014
genomeTreeWorkflow.py		genomeTreeWorkflow.py	Update to v0.9.7. Added unique ids to output tables. Improve quality …	Jan 16, 2015
getHMMs.py		getHMMs.py	Why did Mike delete all my scripts?	Jul 20, 2014
getMarkerGeneHMMs.py		getMarkerGeneHMMs.py	Why did Mike delete all my scripts?	Jul 20, 2014
identifyColocatedGenes.py		identifyColocatedGenes.py	v0.9.4	Sep 9, 2014
identifyCompleteGenomes.py		identifyCompleteGenomes.py	v0.9.4	Sep 9, 2014
identifyDegenerateGenomes.py		identifyDegenerateGenomes.py	v0.9.4	Sep 9, 2014
identifyGeneLossAndDuplication.py		identifyGeneLossAndDuplication.py	Initial implementation to use a reduced reference tree.	Nov 17, 2014
identifyLineageStability.py		identifyLineageStability.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerGeneCorrelation.py		markerGeneCorrelation.py	v0.9.4	Sep 9, 2014
markerSetLOO.py		markerSetLOO.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerSetSelection.py		markerSetSelection.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerSetSize.py		markerSetSize.py	v0.9.4	Sep 9, 2014
markerSetSizes.py		markerSetSizes.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerSetStability.py		markerSetStability.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerSetStabilityTest.py		markerSetStabilityTest.py	Why did Mike delete all my scripts?	Jul 20, 2014
markerSetTest.py		markerSetTest.py	v0.9.4	Sep 9, 2014
plotMarkerSetDistribution.py		plotMarkerSetDistribution.py	v0.9.4	Sep 9, 2014
plotScaffoldLenVsMarkers.py		plotScaffoldLenVsMarkers.py	Why did Mike delete all my scripts?	Jul 20, 2014
pruneTree.py		pruneTree.py	Why did Mike delete all my scripts?	Jul 20, 2014
qcGenomes.py		qcGenomes.py	Why did Mike delete all my scripts?	Jul 20, 2014
runGenomeSigDist.py		runGenomeSigDist.py	Why did Mike delete all my scripts?	Jul 20, 2014
runMarkerSetLOO.py		runMarkerSetLOO.py	Why did Mike delete all my scripts?	Jul 20, 2014
simCompare.py		simCompare.py	Minor bug fixes.	Oct 24, 2014
simCompareDiffPlot.py		simCompareDiffPlot.py	Why did Mike delete all my scripts?	Jul 20, 2014
simComparePlots.py		simComparePlots.py	Fixed issue with ColorbarBase under matplotlib v1.4.0	Oct 9, 2014
simEvaluateBias.py		simEvaluateBias.py	Initial implementation to use a reduced reference tree.	Nov 17, 2014
simEvaluateBiasHistograms.py		simEvaluateBiasHistograms.py	Changed normed to density in Matplotlib hist plots.	May 4, 2020
simInferBestMarkerSet.py		simInferBestMarkerSet.py	Why did Mike delete all my scripts?	Jul 20, 2014
simLineageSpecificMarkerSets.py		simLineageSpecificMarkerSets.py	v0.9.4	Sep 9, 2014
simMarkerGenesVsMarkerSet.py		simMarkerGenesVsMarkerSet.py	v0.9.4	Sep 9, 2014
simTiming.py		simTiming.py	v0.9.4	Sep 9, 2014
simulation.py		simulation.py	Update to v0.9.7. Added unique ids to output tables. Improve quality …	Jan 16, 2015
simulationScaffoldsByLength.py		simulationScaffoldsByLength.py	Move to version 0.9.0.	Sep 4, 2014
simulationScaffoldsRandom.py		simulationScaffoldsRandom.py	Initial implementation to use a reduced reference tree.	Nov 17, 2014
taxonomicTreeWorkflow.py		taxonomicTreeWorkflow.py	Added --pplacer_threads flag to help with peak memory usage. Minor bu…	Nov 3, 2015
tigr2pfam.py		tigr2pfam.py	Why did Mike delete all my scripts?	Jul 20, 2014
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