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():
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()
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))