Copyright I.N.R.A. - C.N.R.S.
emmanuel.courcelle@toulouse.inra.fr jerome.gouzy@toulouse.inra.fr
This software is a computer program whose purpose is to help you run your scripts on parallel computers.
This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL http://www.cecill.info"
As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability.
In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.
The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.
PARALOOP::PLUGIN::Shell - Shell object
PARALOOP::PLUGIN::LnInput
This plugin considers the input file as a list of shell commands: each line is a little script, executed at a given iteration of MainLoop.
The line may have two formats:
1/ <some shell code> 2/ <path_to_an_alternative_interpeter>:<some_code>
When the shell interpreter is not specified (1st format), the shell declared in the parameter PARALOOP_Shell_interpreter is used. The default value is /bin/sh.
when the shell interpreter is specified (2nd format), it is used to execute the rest of the line.
The following is a little input file:
echo -n "Hello Folks, Here is my name: "; hostname /bin/perl : print "Hello Folks, Here is my name: " . `hostname\n`; grep HUMAN file.fasta >file.results
The first 2 lines write something to the Paraloop.pl output file, while the last line writes something to the file called ``file.results''
The first and last lines are executed with /bin/sh, the second is executed with perl
PARALOOP_Shell_interpreter path to the default shell interpreter (default /bin/sh)
WhatParaloopPlugin my $msg=$obj->WhatParaloopPlugin($verbosity);
Parameters my $msg=$obj->Parameters();
New my $obj = PARALOOP::Dummy->New(-params => $params, -log => $o_log);
Exec my ($incr_size,$error,$killed) = $obj->Exec();
SetOutputFile $obj->SetOutputFile('filename');
Usage: my $msg = PARALOOP::Dummy::WhatParaloopPlugin($verbosity) or my $msg = $obj->WhatParaloopPlugin() Function: Return some information (2 lines max) on the plugin An object is NOT considered as a plugin if this function is not implemented Arg: none ($self is ignored) Return: A message describing the plugin (1 or 2 lines)
Usage: my $msg = PARALOOP::Dummy::Parameters() or my $msg = $obj->Parameters() Function: Return the list of allowed parameters for this plugin If your plugin defines some parameters, it is good pratice adding this function, to display those parameters when the --parameters switch of paraloop.pl is used. However, this is not mandatory Arg: none ($self is ignored) Return: A message describing the plugin (1 or 2 lines)
Usage: CALLED BY _Initializable::New my $obj = PARALOOP::Dummy->New(-params => $params, -log => $o_log); Access: private (use New instead) procedure: Init the object Return: nothing Args: -params = an object of class ParamParser (already initialized) -log = an object of class Logger (already initialized) globals: none
Usage: The destructor of the object undef($obj); Access: public procedure: Destroyes the resources allocated by __Init Return: nothing Args: nothing globals: none
Usage: &$opt->SetOutputFile('filename'); Procedure: change the name of the output file Arg : the output file name
Usage: my ($incr_size, $error,$killed) = &$opt->Exec($timeout); Function: Read and execute the next line, using the default shell or the specific shell Arg: $timeout = The number of seconds after which a timeout is sent Return: $incr_size = The number of bytes added to the output file $error = An error code. If != 0, paraloop WILL BE TERMINATED - Generally marks the end of file $killed = A kill code 0: everything OK -1: killed by timeout -2: killed by TERM signal (kill, qdel, ...)