def run_galaxy(ctx, path, job_path, **kwds):
kwds["cwl"] = True
conformance_test = kwds.get("conformance_test", False)
with conditionally_captured_io(conformance_test):
with serve_daemon(ctx, [path], **kwds) as config:
try:
cwl_run = run_cwl_tool(path, job_path, config, **kwds)
except Exception:
io.warn("Problem running cwl tool...")
print(config.log_contents)
raise
print(cwl_run.cwl_command_state)
return 0
def ensure_runnables_served(self, runnables):
# TODO: define an interface for this - not everything in config would make sense for a
# pre-existing Galaxy interface.
with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
yield config
def _serve(self, runnables):
with serve_daemon(self._ctx, runnables,
**self._serve_kwds()) as config:
yield config
def _serve(self, runnables):
with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
yield config
def ensure_runnables_served(self, runnables):
# TODO: define an interface for this - not everything in config would make sense for a
# pre-existing Galaxy interface.
with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
yield config