Python makeRunScript Examples

Example #1

File: configureStrelkaSomaticWorkflow.py Project: zero-raspberry/strelka

def main() :

    primarySectionName="StrelkaSomatic"
    options,iniSections=StrelkaSomaticWorkflowOptions().getRunOptions(primarySectionName,
                                                               version=workflowVersion)

    # we don't need to instantiate the workflow object during configuration,
    # but this is done here to trigger additional parameter validation:
    #
    StrelkaSomaticWorkflow(options)

    # generate runscript:
    #
    ensureDir(options.runDir)
    workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)

    makeRunScript(workflowScriptPath,os.path.join(workflowDir,"strelkaSomaticWorkflow.py"),"StrelkaSomaticWorkflow",primarySectionName,iniSections)

    notefp=sys.stdout
    notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

%s
""" % (workflowScriptPath))

Example #2

File: configureStrelkaNoiseWorkflow.py Project: xuwanxing/strelka

def main() :

    if (sys.version_info[0] != 2):
        notefp=sys.stdout
        notefp.write("""Failed to create workflow run script.\nPyflow only supports python2. Detected python %s on the system.\n""" % sys.version_info[0])
        return

    primarySectionName="snoise"
    options,iniSections=snoiseWorkflowOptions().getRunOptions(primarySectionName, version=workflowVersion)

    # we don't need to instantiate the workflow object during configuration,
    # but this is done here to trigger additional parameter validation:
    #
    snoiseWorkflow(options)

    # generate runscript:
    #
    ensureDir(options.runDir)
    workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)

    makeRunScript(workflowScriptPath,os.path.join(workflowDir,"snoiseWorkflow.py"),"snoiseWorkflow",primarySectionName,iniSections)

    notefp=sys.stdout
    notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

%s
""" % (workflowScriptPath))

Example #3

File: configureSequenceErrorCountsWorkflow.py Project: vasupsu/sprite4

def main():

    primarySectionName = "counts"
    options, iniSections = SequenceErrorCountsWorkflowOptions().getRunOptions(
        primarySectionName, version=workflowVersion)

    # we don't need to instantiate the workflow object during configuration,
    # but this is done here to trigger additional parameter validation:
    #
    SequenceErrorCountsWorkflow(options)

    # generate runscript:
    #
    ensureDir(options.runDir)
    scriptFile = os.path.join(options.runDir, "runWorkflow.py")

    makeRunScript(scriptFile,
                  os.path.join(workflowDir, "sequenceErrorCountsWorkflow.py"),
                  "SequenceErrorCountsWorkflow", primarySectionName,
                  iniSections)

    notefp = sys.stdout
    notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

%s
""" % (scriptFile))

Example #4

File: configManta.py Project: EthidiumIodide/manta

def main() :

    primarySectionName="manta"
    options,iniSections=MantaWorkflowOptions().getRunOptions(primarySectionName, version=workflowVersion)

    # we don't need to instantiate the workflow object during configuration,
    # but this is done here to trigger additional parameter validation:
    #
    MantaWorkflow(options,iniSections)

    # generate runscript:
    #
    ensureDir(options.runDir)
    scriptFile=os.path.join(options.runDir,"runWorkflow.py")

    makeRunScript(scriptFile,os.path.join(workflowDir,"mantaWorkflow.py"),"MantaWorkflow",primarySectionName,iniSections)

    notefp=sys.stdout
    notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

%s
""" % (scriptFile))