cwltool.run_job
===============

.. py:module:: cwltool.run_job

.. autoapi-nested-parse::

   Only used when there is a job script or CWLTOOL_FORCE_SHELL_POPEN=1.



Functions
---------

.. autoapisummary::

   cwltool.run_job.handle_software_environment
   cwltool.run_job.main


Module Contents
---------------

.. py:function:: handle_software_environment(cwl_env, script)

   Update the provided environment dict by running the script.


.. py:function:: 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 specifies 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.