Ubuntu Manpages

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

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


display the list of commands.

get version

specify configuration file

sequence file to analyse.

grammar file to analyse

model file to analyse

analyse dna, is default

analyse rna

analyse protein

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)