Provided by: logol_1.7.9-1_all
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.
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 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)
Olivier Sallou (olivier.sallou (at) irisa.fr)