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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)
