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)