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.
LogolMultiExec [-h]
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
LogolMultiExec and LogolExec share the same configuration file. See LogolExec man page for more info. .PP
Minimum arguments are -m for logol model or -g for logol grammar, and -s for input sequence
-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 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
-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)
Olivier Sallou (olivier.sallou (at) irisa.fr)