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===== sp_batch =====
Batch Pipeline Execution: Run jobs that wait with the execution on each other.

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===== Usage =====

Usage in command line

  sp_batch.py  submission_command  input_run_dir --hold_flag=HOLD_FLAG --first_hold_number=FIRST_HOLD_NUMBER
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===== Typical usage =====

sp_batch exists only in non-MPI version.

The pipeline directory can be easily added within the GUI.

Run sp_batch locally with bash:

  sp_batch.py bash input_run_dir

Run sp_batch within a SGE/PBS/Torque queuing environment:

  sp_batch.py 'qsub' input_run_dir --hold_flag='-hold_jid'

Run sp_batch within a SGE/PBS/Torque queuing environment waiting for another job with the id 3456:

  sp_batch.py 'qsub' input_run_dir --hold_flag='-hold_jid' --first_hold_number=3456

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===== Input =====
=== Main Parameters ===
  ; submission_command : Submission command : Submission command, e.g., qsub, qsub -V, sbatch, bash (default required string)
  ; input_run_dir: Pipeline directory : Directory containin the pipeline submission files (default required string)
  ; %%--%%hold_flag: Hold flag: Hold flag for the submission command, e.g. -hold_jid=, --wait=, --dependency=afterany:; Default is None and should be used in combination with a local execution with bash (default none)
  ; %%--%%first_hold_number: First hold number : Wait number for the first job that is submitted. By default, the first job will not wait for others (default none)

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===== Output =====
Content of the commands in the PIPELINE folder.

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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====

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==== Author / Maintainer ====
Markus Stabrin

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_unblur.py

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==== See also ====

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==== Maturity ====
Beta:: Under evaluation and testing. Please let us know if there are any bugs.

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==== Bugs ====
There are no known bugs so far.

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