Man pages sections > man1 > LogolMultiExec

LogolMultiExec - Program to parse a logol grammar and search pattern in a

LogolMultiExec(1) USER COMMANDS LogolMultiExec(1)

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)
 
September 28, 2011 version 1.0