:py:mod:`km3pipe.shell`
=======================

.. py:module:: km3pipe.shell

.. autoapi-nested-parse::

   Some shell helpers

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Module Contents
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Classes
~~~~~~~

.. autoapisummary::

   km3pipe.shell.Script



Functions
~~~~~~~~~

.. autoapisummary::

   km3pipe.shell.qsub
   km3pipe.shell.submit
   km3pipe.shell.gen_job
   km3pipe.shell.get_jpp_env



Attributes
~~~~~~~~~~

.. autoapisummary::

   km3pipe.shell.log
   km3pipe.shell.BATCH_TYPE
   km3pipe.shell.SUBMIT_CMD
   km3pipe.shell.JOB_TEMPLATES


.. py:data:: log

   

.. py:data:: BATCH_TYPE

   

.. py:data:: SUBMIT_CMD

   

.. py:data:: JOB_TEMPLATES

   

.. py:function:: qsub(script, job_name, dryrun=False, silent=False, *args, **kwargs)

   
   Submit a job via qsub.

   Returns the job script as string.















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.. py:function:: submit(script, job_name, dryrun=False, silent=False, *args, **kwargs)

   
   Submit a job.

   Returns the job script as string.















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.. py:function:: gen_job(script, job_name, log_path='qlogs', group='km3net', walltime='00:10:00', nodes=1, ppn=4, node_type=None, cluster='in2p3', memory='3G', email=None, send_mail='n', job_array_start=1, job_array_stop=None, job_array_step=1, irods=False, sps=True, hpss=False, xrootd=False, dcache=False, oracle=False, split_array_logs=False)


.. py:function:: get_jpp_env(jpp_dir)

   
   Return the environment dict of a loaded Jpp env.

   The returned env can be passed to `subprocess.Popen("J...", env=env)`
   to execute Jpp commands.















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.. py:class:: Script




   
   A shell script which can be built line by line for `qsub`.
















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   .. py:method:: add(line)

      
      Add a new line
















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   .. py:method:: echo(text)

      
      Add an echo command. The given text will be double qouted.
















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   .. py:method:: separator(character='=', length=42)

      
      Add a visual separator.
















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   .. py:method:: cp(source, target)

      
      Add a new copy instruction
















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   .. py:method:: mv(source, target)

      
      Add a new move instruction
















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   .. py:method:: mkdir(folder_path)

      
      Add a new 'mkdir -p' instruction
















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   .. py:method:: iget(irods_path, attempts=1, pause=15)

      
      Add an iget command to retrieve a file from iRODS.


      :Parameters:

          **irods_path: str**
              Filepath which should be fetched using iget

          **attempts: int (default: 1)**
              Number of retries, if iRODS access fails

          **pause: int (default: 15)**
              Pause between two access attempts in seconds














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   .. py:method:: clear()