NAME
    Runner::Init

VERSION
    Version 0.01

SYNOPSIS
    This is a base class for Runner::MCE and Runner:Threads. You should not
    need to call this module directly.

EXPORT
VARIABLES
  infile
    File of commands separated by newline. The command 'wait' indicates all
    previous commands should finish before starting the next one.

  outdir
    Directory to write out files and logs.

  logdir
    Pattern to use to write out logs directory. Defaults to
    outdir/prunner_current_date_time/log1 .. log2 .. log3.

  procs
    Total number of running children allowed at any time. Defaults to 10.
    The command 'wait' can be used to have a variable number of children
    running. It is best to wrap this script in a slurm job to not overuse
    resources. This isn't used within this module, but passed off to
    mcerunner/parallelrunner.

Internal VARIABLES
    You shouldn't be calling these directly.

Subroutines
  run_commands_threads
    Start the thread, run the command, and finish the thread

  run_commands_mce
    MCE knows which subcommand to use from Runner/MCE - object mce

  _log_commands
    Log the commands run them. Cat stdout/err with IO::Select so we
    hopefully don't break things.

    This example was just about 100% from the following perlmonks
    discussions.

    http://www.perlmonks.org/?node_id=151886

    You can use the script at the top to test the runner. Just download it,
    make it executable, and put it in the infile as

    perl command.pl 1 perl command.pl 2 #so on and so forth

AUTHOR
    Jillian Rowe, "<jillian.e.rowe at gmail.com>"

BUGS
    Please report any bugs or feature requests to "bug-runner-init at
    rt.cpan.org", or through the web interface at
    <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Runner-Init>. I will be
    notified, and then you'll automatically be notified of progress on your
    bug as I make changes.

SUPPORT
    You can find documentation for this module with the perldoc command.

        perldoc Runner::Init

    You can also look for information at:

    *   RT: CPAN's request tracker (report bugs here)

        <http://rt.cpan.org/NoAuth/Bugs.html?Dist=Runner-Init>

    *   AnnoCPAN: Annotated CPAN documentation

        <http://annocpan.org/dist/Runner-Init>

    *   CPAN Ratings

        <http://cpanratings.perl.org/d/Runner-Init>

    *   Search CPAN

        <http://search.cpan.org/dist/Runner-Init/>

ACKNOWLEDGEMENTS
    This module was originally developed at and for Weill Cornell Medical
    College in Qatar. With approval from WCMC-Q, this information was
    generalized and put on github, for which the authors would like to
    express their gratitude.

LICENSE AND COPYRIGHT
    Copyright 2014 Jillian Rowe.

    This program is free software; you can redistribute it and/or modify it
    under the terms of the the Artistic License (2.0). You may obtain a copy
    of the full license at:

    <http://www.perlfoundation.org/artistic_license_2_0>

    Any use, modification, and distribution of the Standard or Modified
    Versions is governed by this Artistic License. By using, modifying or
    distributing the Package, you accept this license. Do not use, modify,
    or distribute the Package, if you do not accept this license.

    If your Modified Version has been derived from a Modified Version made
    by someone other than you, you are nevertheless required to ensure that
    your Modified Version complies with the requirements of this license.

    This license does not grant you the right to use any trademark, service
    mark, tradename, or logo of the Copyright Holder.

    This license includes the non-exclusive, worldwide, free-of-charge
    patent license to make, have made, use, offer to sell, sell, import and
    otherwise transfer the Package with respect to any patent claims
    licensable by the Copyright Holder that are necessarily infringed by the
    Package. If you institute patent litigation (including a cross-claim or
    counterclaim) against any party alleging that the Package constitutes
    direct or contributory patent infringement, then this Artistic License
    to you shall terminate on the date that such litigation is filed.

    Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER
    AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES.
    THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
    PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY
    YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR
    CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
    CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
    EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

