def get_job_file(self, job_wrapper, **kwds): job_metrics = job_wrapper.app.job_metrics job_instrumenter = job_metrics.job_instrumenters[job_wrapper.job_destination.id] env_setup_commands = kwds.get("env_setup_commands", []) env_setup_commands.append(job_wrapper.get_env_setup_clause() or "") destination = job_wrapper.job_destination or {} envs = destination.get("env", []) envs.extend(job_wrapper.environment_variables) for env in envs: env_setup_commands.append(env_to_statement(env)) command_line = job_wrapper.runner_command_line options = dict( job_instrumenter=job_instrumenter, galaxy_lib=job_wrapper.galaxy_lib_dir, galaxy_virtual_env=job_wrapper.galaxy_virtual_env, env_setup_commands=env_setup_commands, working_directory=os.path.abspath(job_wrapper.working_directory), command=command_line, shell=job_wrapper.shell, ) # Additional logging to enable if debugging from_work_dir handling, metadata # commands, etc... (or just peak in the job script.) job_id = job_wrapper.job_id log.debug("(%s) command is: %s" % (job_id, command_line)) options.update(**kwds) return job_script(**options)
def get_job_file(self, job_wrapper, **kwds): job_metrics = job_wrapper.app.job_metrics job_instrumenter = job_metrics.job_instrumenters[ job_wrapper.job_destination.id] env_setup_commands = kwds.get('env_setup_commands', []) env_setup_commands.append(job_wrapper.get_env_setup_clause() or '') destination = job_wrapper.job_destination or {} envs = destination.get("env", []) envs.extend(job_wrapper.environment_variables) for env in envs: env_setup_commands.append(env_to_statement(env)) command_line = job_wrapper.runner_command_line options = dict( job_instrumenter=job_instrumenter, galaxy_lib=job_wrapper.galaxy_lib_dir, galaxy_virtual_env=job_wrapper.galaxy_virtual_env, env_setup_commands=env_setup_commands, working_directory=os.path.abspath(job_wrapper.working_directory), command=command_line, shell=job_wrapper.shell, ) # Additional logging to enable if debugging from_work_dir handling, metadata # commands, etc... (or just peak in the job script.) job_id = job_wrapper.job_id log.debug('(%s) command is: %s' % (job_id, command_line)) options.update(**kwds) return job_script(**options)
def get_job_file(self, job_wrapper, **kwds): options = dict( galaxy_lib=job_wrapper.galaxy_lib_dir, env_setup_commands=job_wrapper.get_env_setup_clause(), working_directory=os.path.abspath( job_wrapper.working_directory ), command=job_wrapper.runner_command_line, ) options.update(**kwds) return job_script(**options)