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

# LogolExec(1)

Program to parse a logol grammar and search pattern in a sequence.

## NAME

LogolExec - Program to parse a logol grammar and search pattern in a sequence.

## SYNOPSIS

**LogolExec** \[-h\]

## INSTALLATION

 Logol requires the Cassiopee Ruby gem. To install it run:\
  gem install cassiopee

## CONFIGURATION

 LogolExec use a default configuration file in /etc/logol/logol.properties. It is possible to specify a different configuration file via command-line. Temporary and results directory must be writable by the user.\
  By default, /var/lib/logol/results contains generated results and /tmp is used at temporary directory.\
  .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

- \-check

   check a grammar, no execution. Requires -g

- \-dna

   analyse dna, is default

- \-rna

   analyse rna

- \-protein

   analyse protein

- \-max

    maximum returned solutions

- \-all

   analyse both directions of the sequence

- \-output

   output file name, must be unique

### OTHER OPTIONS

- \-sequenceID

   position of sequence in bank

- \-uid

   Use a defined identifier for the query

- \-lmax

   maximum length of a variable

- \-maxspacer

   maximum size of a spacer

- \-offset

   Offset value to add to positions

- \-start

   Start position on sequence

- \-end

   End position on sequence

- \-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)

- \-c

   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)