Esempio n. 1
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    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)
Esempio n. 2
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    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)