.TH LogolExec 1  "September 28, 2011" "version 1.0" "USER COMMANDS"
.SH NAME
LogolExec \- Program to parse a logol grammar and search pattern in a sequence.
.SH SYNOPSIS
.B LogolExec
[\-h]
.PP
.SH INSTALLATION
 Logol requires the Cassiopee Ruby gem. To install it run:
 gem install cassiopee
.SH CONFIGURATION
 LogolExec use a default configuration file in /etc/logol/logol.properties.
It is possible to specify a different configuration file via command-line.
Temporary and results directory must be writable by the user.
 By default, /var/lib/logol/results contains generated results and /tmp is
used at temporary directory.
 .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
\-check
 check a grammar, no execution. Requires \-g
.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
\-output
 output file name, must be unique
.PP
.SS OTHER OPTIONS
.TP
\-sequenceID
 position of sequence in bank
.TP
\-uid
 Use a defined identifier for the query
.TP
\-lmax
 maximum length of a variable
.TP
\-maxspacer
 maximum size of a spacer
.TP
\-offset
 Offset value to add to positions
.TP
\-start
 Start position on sequence
.TP
\-end
 End position on sequence
.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
\-c
 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)