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.

SYNOPSIS

       LogolMultiExec [-h]

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

CONFIGURATION

        LogolMultiExec and LogolExec share the same configuration file. See LogolExec man page for more info.
        .PP

OPTIONS

        Minimum arguments are -m for logol model or -g for logol grammar, and -s for input sequence

   MAIN OPTIONS
       -h
               display the list of commands.

       -v
               get version

       -conf
               specify configuration file

       -s
               sequence file to analyse.

       -g
               grammar file to analyse

       -m
               model file to analyse

       -dna
               analyse dna, is default

       -rna
               analyse rna

       -protein
               analyse protein

       -max
                maximum returned solutions

       -all
               analyse both directions of the sequence

       -out
               Zip output file name

       -fasta
               Add fasta conversion of the matches to the result archive

       -contig
               Set the input bank as contig sequences

       -guid
               Unique identifier for the query

       -email
               Email address to sent result availability info
               (needs mail setup)

       -local
               Use local mode (multi core)

       -sge
               Use SGE mode

       -forcesplit
               Force the sequence splitting according to parameters and whatever is the number of model used  in
              grammar

   OTHER OPTIONS
       -lmax
               maximum length of a variable

       -maxspacer
               maximum size of a spacer

       -noclean
               Do not delete created files after treatment (for debug)

       -enabledups
               enable duplicate result matches. By default only keep singletons

       -filter
               Type     of     filter     when    enabledups    is    not    enabled.    Allowed    types    are
              exact(default),local,local0,global.

       -lmin
               minimum length of a variable (to speedup parsing)

       -maxmatchsize
               maximum size of a match (to speedup parsing)

       -maxres
               maximum result size of a match  (to speedup parsing)

AUTHOR

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