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::Bioperl - Executing something with files read using bioperl
PARALOOP::PLUGIN::BpInput
This plugin reads the next record from the input file, whose format must be recognized by bioperl, calls an external program or script, then writes the output of this program
The external script is passed as: script_name param1 param2 ... input output, ie the last two parameters are the input and the output file, the other parameters are declared by PARAMETER_Bioperl_params
Please note that when the script is ran, its current directory is a temporary directory, located in the same directory as the input file. You may securely create files here.
PARALOOP_Bioperl_path path to the external script, ran at each iteration. No default PARALOOP_Bioperl_params parameters passed to this script. Default 0 PARALOOP_Bioperl_input_format Format for the input file (default to fasta) WARNING - This is the format to the file which is read by THE EXTERNAL script BUT the input file from paraloop may be of any format automatically recognized by bioperl
The following is a very stupid script, which makes nothing which could be executed through this plugin:
#!/bin/sh
sleep $1; cat $2 > $3 exit 0;
If the script is called stupid.sh and lives in the current paraloop directory, there should be two parameters defined:
PARALOOP_Bioperl_path = stupid.sh PARALOOP_Bioperl_params = 3
The script is called by paraloop as:
stupid.sh 3 input output
WhatParaloopPlugin my $msg=$obj->WhatParaloopPlugin()
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() 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 => $o_log); Access: private (use New instead) procedure: Init the object Return: nothing Args: -params = an object of class ParamParser (already initialized) -log = an object of class Logger (already initialized) globals: none
Usage: &$opt->SetOutputFile('filename'); Procedure: change the name of the output file Arg : the output file name
Usage: The destructor of the object undef($obj); Access: public procedure: Destroyes the resources allocated by __Init Return: nothing Args: nothing globals: none
Usage: my ($incr_size, $error,$killed) = &$opt->Exec($timeout); Function: Execute the external script 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, ...)