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"
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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.
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PARALOOP::PLUGIN::Blast - Executing blast (any version)
PARALOOP::PLUGIN::BpInput
This plugin reads the next record from the fasta input file, uses this file as a query for a blastall -p request agains the bank, passed through the --db switch The tabular output is chosen
PARALOOP_Blast_origin ncbi or wu: both are supported, but default is ncbi PARALOOP_Blast_path path to the binary program (default blastall if ncbi, blastp if wu) PARALOOP_Blast_params Parameters for blast (default -p blastp if ncbi, nothing if wu) PARALOOP_Blast_chunk Group requests in chunks for a better efficiency (default 1, ie not grouped)
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 UNIVERSAL::New my obj = PARALOOP::Dummy->New(-params => $params, -log => $o_log); Access: protected (use New instead) procedure: Init the object Return: nothing Args: -params = an object of class ParamParser (already initialized) -log = an object of class Logger (already initialized) globals: none
Usage: &$opt->SetOutputFile('filename'); Procedure: change the name of the output file Arg : the output file name
Usage: my ($incr_size, $error,$killed) = &$opt->Exec($timeout); Function: Execute a blast 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 $killed = A kill code 0: everything OK -1: killed by timeout -2: killed by TERM signal (kill, qdel, ...)
Usage: my ($incr_size, $error,$killed) = &self->__SingleSeq($timeout); Function: Called by Exec when blasts are made sequence by sequence Arg, Return: see Exec
Usage: my ($incr_size, $error,$killed) = &self->__SeveralSeq($timeout); Function: Called by Exec when blasts are made in chunks of sequences Arg, Return: see Exec
Usage: my $sts = $obj->StealWork($o_scheduler) function: Look inside all the jobs, trying to steal some work to another job. 1/ Look for the jobs whose status is anything but TERMINATED or INTERRUPTED 2/ Select the less advanced job 3/ If this job has a more than 1 record (configurable with PARALOOP_load_balancing_threshold parameter), submit a new monoprocessor job, taking 50% of the remaining work This function may be overloaded by the plugins, if necessary. precondition: $o_scheduler must exist and be initialized Return: 0 if nothing stolen, 1 if something stolen Args: $o_scheduler Globals: none