The command line

The only user interface of Teolenn is the command line. The syntax and the available options can be get using the following command :

$ teolenn.sh -h

The program show you the following output:

usage: teolenn [options] design [genome [genome_masked [output_dir]]]
 -about              display information about this software
 -conf <file>        configuration file to use
 -h,--help           display this help
 -license            display information about the license of this
                     software
 -log <file>         external log file
 -loglevel <level>   log level
 -silent             don't show log on console
 -threads <number>   number of threads to use
 -v,--verbose        display external tools output
 -version            show version of the software

arguments

The Teolenn command line has 4 standards arguments (without options) that overwrite parameters of the design file:

  • design: This is the design file to read. This file contains all the parameters to run the design. This is the only argument of Teolenn that is mandatory.
  • genome: Is the path to the genome file (one file in fasta format). This argument is optional as this parameter can be set in the design file.
  • genome_masked: Is the path to the genome masked file (one file in fasta format). This argument is optional as this parameter can be set in the design file.
  • output_dir: Is the output directory for the file generated by Teolenn.

-about

When you run Teolenn with this option, you will get information about this software and then returns to the shell.

-conf <file>

With this option, Teolenn will load the file as configuration file. See the configuration section for more information.

-license

When you run Teolenn with this option, you will get information about Teolenn license and and then returns to the shell.

-log <file>

Define the log file.

-loglevel <level>

Set the log level, there are 4 log level define in Teolenn : Severe, Warning, Info and Fine. By default the log level is set to Info

-silent

Don't show log on the console.

-threads

Set the number of threads to use use when compute design. By default the value is set to the number of available processor (cores in multi-cores processor). If the value is lower than 1, use the default value.

-v

When this option is enable, the output of external tools used by Teolenn will be displayed on the console.

-version

When you run Teolenn with this option, you will get information about Teolenn version and and then returns to the shell.

Teolenn configuration file

Some global parameters of Teolenn such as the path of the external tools can be set in a configuration file. There are two ways to use this configuration file:

  • Create a ~/.teolenn file.
  • use the -conf <file> option of Teolenn command line. The ~/.teolenn file will not be read.

The next table summaries the available parameters for Teolenn configuration file:

Parameter Type Description
soap.path String The soap executable path. By default Teolenn use the version embedded if exists for your platform. When this parameter is set the embedded version will not be used.
gt.path String The genometools executable path. By default Teolenn use the version embedded if exists for your platform. When this parameter is set the embedded version will not be used.
std.output Boolean Show the output of the external executable. This parameter as the same effect than -v option of Teolenn command line.
max.threads Integer Set the maximal number of threads. This parameter as the same effect than -threads option of Teolenn command line.

Teolenn configuration file sample

# This is an example of configuration file for Teolenn.
# You need to use the -conf parameter or rename this file to
# $HOME/.teolenn to enable it.

# SOAP path.
# By default Teolenn use the its embedded version if exists for your platform.
soap.path=/usr/local/soap/soap

# Genome tools path.
# By default Teolenn use the its embedded version if exists for your platform.
gt.path=/usr/local/gt/gt

# Show the output of external executable to the user.
std.output=false

# Set the maximal number of threads.
# If value if <1 Teolenn use the available processor as value.
max.threads=-1