: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.gen_job
   km3pipe.shell.get_jpp_env
















































.. data:: log
   

   









.. data:: JOB_TEMPLATE
   

   









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

   
   Submit a job via qsub.















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.. function:: gen_job(script, job_name, log_path='qlogs', group='km3net', platform='cl7', walltime='00:10:00', vmem='8G', fsize='8G', shell=None, 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)

   
   Generate a job script.















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.. 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

   Bases::class:`object`

   

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















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   .. method:: add(self, line)

      
      Add a new line















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   .. method:: echo(self, text)

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















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

      
      Add a visual separator.















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

      
      Add a new copy instruction















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

      
      Add a new move instruction















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   .. method:: mkdir(self, folder_path)

      
      Add a new 'mkdir -p' instruction















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   .. method:: iget(self, 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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   .. method:: clear(self)