cwltool.run_job¶
Only used when there is a job script or CWLTOOL_FORCE_SHELL_POPEN=1.
Module Contents¶
Functions¶
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Update the provided environment dict by running the script. |
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Read in the configuration JSON and execute the commands. |
- cwltool.run_job.handle_software_environment(cwl_env, script)¶
Update the provided environment dict by running the script.
- Parameters
cwl_env (Dict[str, str]) –
script (str) –
- Return type
Dict[str, str]
- cwltool.run_job.main(argv)¶
Read in the configuration JSON and execute the commands.
- The first argument is the path to the JSON dictionary file containing keys:
“commands”: an array of strings that represents the command line to run “cwd”: A string specifying which directory to run in “env”: a dictionary of strings containing the environment variables to set “stdin_path”: a string (or a null) giving the path that should be piped to STDIN “stdout_path”: a string (or a null) giving the path that should receive the STDOUT “stderr_path”: a string (or a null) giving the path that should receive the STDERR
- The second argument is optional, it specifes a shell script to execute prior,
and the environment variables it sets will be combined with the environment variables from the “env” key in the JSON dictionary from the first argument.
- Parameters
argv (List[str]) –
- Return type
int