---
name: "LogolMultiExec"
section: "1"
platform: "linux"
package: "logol"
version: "1.7.9+dfsg-6"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/LogolMultiExec"
---

# LogolMultiExec(1)

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.

## 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)