def main(): genome_file = LocalFile( label = 'E. coli K12 DH10B genome', \ path = SAMPLE_GENOME ) genome_file.save() ## This gives a reference to the tool (which you probably don't want to modify.) prodigal = StandaloneTool.objects.get( name='Prodigal', version='2.60' ) ## this should actually instantiate the entire flow and children, with blueprints # never being seen by the user. ## All commands and subflows are instantiated and saved to the database, and the # parent flow is returned. This will almost never pass an is_ready() check since # no required parameters have been set yet. flow = prodigal.new_flow() flow.save() command = flow.get_command(name='Run prodigal') command.set_param(name='-i', val=genome_file.path) command.set_param(name='-o', val='/tmp/prodigal.test.out' ) command.set_param(name='-g', val='10' ) flow.run() while flow.is_executing(): flow = Flow.objects.get(id=flow.id) print("Gene prediction state is: {0}".format(flow.get_state_display()) ) sleep(1) output = command.get_param( name='-o' ) print("{0} completed. Output written to: {1}".format(command.name, output.value))
def main(): workspace = Workspace( name = 'Example tool discovery and diginorm' ) workspace.save() left_reads = LocalFile( label = 'Left sample reads', path = SAMPLE_LEFT_READS ) left_reads.save() right_reads = LocalFile( label = 'Right sample reads', path = SAMPLE_RIGHT_READS ) right_reads.save() #workspace.add( left_reads, right_reads ) workspace.add_data( left_reads ) workspace.add_data( right_reads ) tools_available = workspace.get_available_tools() for tool in tools_available: print("{0}".format(tool))
def main(): workspace = Workspace(name='Example tool discovery and diginorm') workspace.save() left_reads = LocalFile(label='Left sample reads', path=SAMPLE_LEFT_READS) left_reads.save() right_reads = LocalFile(label='Right sample reads', path=SAMPLE_RIGHT_READS) right_reads.save() #workspace.add( left_reads, right_reads ) workspace.add_data(left_reads) workspace.add_data(right_reads) tools_available = workspace.get_available_tools() for tool in tools_available: print("{0}".format(tool))
def main(): genome_file = LocalFile( label = 'E. coli K12 DH10B genome', \ path = SAMPLE_GENOME ) genome_file.save() ## This gives a reference to the tool (which you probably don't want to modify.) prodigal = StandaloneTool.objects.get( name='Prodigal', version='2.60' ) ## this should actually instantiate the entire flow and children, with blueprints # never being seen by the user. ## All commands and subflows are instantiated and saved to the database, and the # parent flow is returned. This will almost never pass an is_ready() check since # no required parameters have been set yet. flow = prodigal.new_flow() command = flow.get_command(name='Run prodigal') command.set_param(name='-i', val=genome_file.path) command.set_param(name='-o', val='/tmp/prodigal.test.out' ) command.set_param(name='-g', val='10' ) flow.run()