.TH LogolMultiExec 1  "September 28, 2011" "version 1.0" "USER COMMANDS"
.SH NAME
LogolMultiExec \- Program to parse a logol grammar and search pattern in a sequence, it
allows one to run the LogolExec program on multi fasta input and to dispatch the treatements
 on a DRMAA compliant grid or on multi-cpu servers.
.SH SYNOPSIS
.B LogolMultiExec
[\-h]
.PP
.SH INSTALLATION
 LogolMultiExec needs the drmaa library. Default is to use SGE library. If another is used,
 one should update the symbolic link in  /usr/share/logol/lib/drmaa.jar to the correct library.
 LD_LIBRARY_PATH must also updated in /sur/share/logol/LogolMultiExec.sh
.SH CONFIGURATION
 LogolMultiExec and LogolExec share the same configuration file. See LogolExec man page for more info.
 .PP
.SH OPTIONS
 Minimum arguments are \-m for logol model or \-g for logol grammar, and \-s for input sequence
.SS MAIN OPTIONS
.TP
\-h
 display the list of commands.
.TP
\-v
 get version
.TP 
\-conf
 specify configuration file
.TP 
\-s
 sequence file to analyse.
.TP
\-g
 grammar file to analyse
.TP
\-m
 model file to analyse
.TP
\-dna
 analyse dna, is default
.TP
\-rna
 analyse rna
.TP
\-protein
 analyse protein
.TP
\-max
  maximum returned solutions
.TP
\-all
 analyse both directions of the sequence
.TP
\-out
 Zip output file name
.TP
\-fasta
 Add fasta conversion of the matches to the result archive
.TP
\-contig
 Set the input bank as contig sequences
.TP
\-guid
 Unique identifier for the query
.TP
\-email
 Email address to sent result availability info
 (needs mail setup)
.TP
\-local
 Use local mode (multi core)
.TP
\-sge
 Use SGE mode
.TP
\-forcesplit
 Force the sequence splitting according to parameters and whatever is the number of model used in grammar
.PP
.SS OTHER OPTIONS
.TP
\-lmax
 maximum length of a variable
.TP
\-maxspacer
 maximum size of a spacer
.TP
\-noclean
 Do not delete created files after treatment (for debug)
.TP
\-enabledups
 enable duplicate result matches. By default only keep singletons
.TP
\-filter
 Type of filter when enabledups is not enabled. Allowed types are exact(default),local,local0,global.
.TP
\-lmin
 minimum length of a variable (to speedup parsing)
.TP
\-maxmatchsize
 maximum size of a match (to speedup parsing)
.TP
\-maxres
 maximum result size of a match  (to speedup parsing)
.PP


.SH AUTHOR
Olivier Sallou (olivier.sallou (at) irisa.fr)