LogolMultiExec1
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.
Usage
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)
Releases
Unchanged in 5 releases since Debian 8 (Jessie).