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
The Teolenn command line has 4 standards arguments (without options) that overwrite parameters of the design file:
When you run Teolenn with this option, you will get information about this software and then returns to the shell.
With this option, Teolenn will load the file as configuration file. See the configuration section for more information.
When you run Teolenn with this option, you will get information about Teolenn license and and then returns to the shell.
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
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.
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:
~/.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. |
# 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