How to use the cellbrowser.copyPkgFile function in cellbrowser

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github maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github external
def cbTrackHub(options):
    " make track hub given meta file and directory with bam files "
    if options.init:
        cellbrowser.copyPkgFile("sampleConfig/cellbrowser.conf")
        sys.exit(0)

    if isfile(options.inConf):
        conf = cellbrowser.loadConfig(options.inConf)

        db = conf["ucscDb"]
        inMatrixFname = conf["exprMatrix"]
        metaFname = conf["meta"]
        clusterFieldName = conf["clusterField"]
        clusterOrderFile = conf.get("clusterOrder")
        bamDir = conf.get("bamDir", "bam")
        fixDot = conf.get("fixDot", False)
        email = conf.get("hubEmail", CBEMAIL)
        geneType = conf["geneIdType"]
        outDir = conf["hubDir"]
        unitName = conf.get("unit", "TPM")