def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
# TODO: convert UI to runnable and do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
# TODO: convert UI to runnable and do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def for_runnable_identifier(ctx,
runnable_identifier,
kwds,
temp_path=None,
return_all=False):
"""Convert URI, path, or alias into Runnable."""
# could be a URI, path, or alias
current_profile = kwds.get('profile')
runnable_identifier = translate_alias(ctx, runnable_identifier,
current_profile)
if not runnable_identifier.startswith(GALAXY_WORKFLOWS_PREFIX):
runnable_identifier = uri_to_path(ctx, runnable_identifier)
if os.path.exists(runnable_identifier):
runnable = for_path(runnable_identifier,
temp_path=temp_path,
return_all=return_all)
else: # assume galaxy workflow id
if not runnable_identifier.startswith(GALAXY_WORKFLOWS_PREFIX):
runnable_identifier = f"{GALAXY_WORKFLOWS_PREFIX}{runnable_identifier}"
runnable = for_uri(runnable_identifier)
return runnable
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
kwds["cwl"] = path.endswith(".cwl")
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
kwds["cwl"] = path.endswith(".cwl")
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, runnable_identifier, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
runnable_identifier = translate_alias(ctx, runnable_identifier,
kwds.get('profile'))
path = uri_to_path(ctx, runnable_identifier)
if os.path.exists(path):
runnable = for_path(path)
else: # assume galaxy workflow id
runnable = for_id(runnable_identifier)
# TODO: do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
if is_cwl:
kwds["engine"] = "cwltool"
elif kwds.get('galaxy_url', None):
kwds["engine"] = "external_galaxy"
else:
kwds["engine"] = "galaxy"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(runnable, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0