The command line

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

$ eoulsan.sh -h

The program show you the following output:

usage: eoulsan [options] action arguments
 -about                display information about this software
 -conf <file>          configuration file to use
 -h,--help             display this help
 -j <path>             JAVA_HOME path
 -J <args>             JVM arguments (-server by default)
 -license              display information about the license of this
                       software
 -log <file>           external log file
 -loglevel <level>     log level
 -m <size>             maximal memory usage for JVM in MB (4096 by default)
 -p <classpath>        additional classpath for eoulsan plugins
 -s <property=value>   set a configuration setting. This option can be
                       used several times
 -version              show version of the software
Available actions:
 - emrexec      execute eoulsan on Amazon Elastic MapReduce service.
 - createdesign create a design file from a list of files.
 - createhadoopjar      create a jar file for hadoop with all dependencies include.
 - exec execute Eoulsan in local mode.
 - hadoopexec   execute Eoulsan on local hadoop cluster.

Actually, Eoulsan has 5 available actions:

  • emrexec: Upload data and launch Eoulsan analysis on Amazon Web Services cloud.
  • exec: Launch Eoulsan analysis in local mode.
  • hadoopexec: Launch Eoulsan analysis on a Hadoop cluster.
  • createdesign: Create a design file from a list of fastq, gff and fasta files.
  • createhadoopjar: Create an Eoulsan jar file that contains all jar dependencies. This jar file can be used to run manualy Eoulsan on a Hadoop cluster (local or in Amazon Web Services cloud).

You can display general help and specific help about an action using -h argument.

-about

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

-conf <file>

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

-s <property=value>

With this option, Eoulsan will set a specific setting. Usage of this option override settings loaded in configuration file. Key and value of the setting are separated by the '=' character. This option can be used several times in command line. See the configuration section for more information.

-j <path>

This option allow to define the path to the JVM to use for running Eoulsan.

-J <args>

Define the JVM options when running Eoulsan. The default value is "-server".

-license

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

-log <file>

Define the log file.

-loglevel <level>

Set the log level, there are 5 log level define in Eoulsan : Severe, Warning, Info, Fine and all. By default the log level is set to Info.

-m <size>

Define the maximal size in megabytes that can be allocated by the JVM. The default value is 4096.

-p <classpath>

Define additional classpath for Eoulsan plug-ins or dependencies.

-version

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

Environment variables

In order to avoid modify the eoulsan.sh file, you use the following environment variable to configure Eoulsan JVM and plugins path:

  • EOULSAN_JAVA_HOME: The path to the JDK to use with Eoulsan. If this environment variable is not set the JAVA_HOME environment varibale will be used. If none of this environment variables is set, the default java command will be used to launch Eoulsan.
  • EOULSAN_MEMORY: The maximum size in MiB of the JVM memory allocation pool. Default value is 4096.
  • EOULSAN_JVM_OPTS: The JVM options. Default value is "-server".
  • EOULSAN_PLUGINS: The path to Eoulsan plugins. No default value is set.