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 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
display the list of commands.
specify configuration file
sequence file to analyse.
grammar file to analyse
model file to analyse
analyse dna, is default
maximum returned solutions
analyse both directions of the sequence
Zip output file name
Add fasta conversion of the matches to the result archive
Set the input bank as contig sequences
Unique identifier for the query
Email address to sent result availability info (needs mail setup)
Use local mode (multi core)
Use SGE mode
Force the sequence splitting according to parameters and whatever is the number of model used in grammar
maximum length of a variable
maximum size of a spacer
Do not delete created files after treatment (for debug)
enable duplicate result matches. By default only keep singletons
Type of filter when enabledups is not enabled. Allowed types are exact(default),local,local0,global.
minimum length of a variable (to speedup parsing)
maximum size of a match (to speedup parsing)
maximum result size of a match (to speedup parsing)
Olivier Sallou (olivier.sallou (at) irisa.fr)