Basic User Guide

module, or softwares as plug-in

Environment module allows you to dynamically set up your working environment using modulefiles

Each modulefile contains the necessary information to set up your shell for the use of a given bioinfo package. Basically this describe the environment changes (PATH, MANPATH, LDFLAGS, environment variables, and so on...) that will be performed at the modulefile loading

modulefiles are provided for all the software packages installed on the central cluster.

In a programmatic way:

  • module allows you to load on demand one or more software package(s) available on the cluster. You can even specify the package version.
  • module allows you to dynamicaly change your working environment.
  • modulefiles can be loaded or unloaded unsing a simple command line.
  • use module av in order to display available modules on the cluster
  • use module load module_name to load given module and access tools from the corresponding package.
  • use module unload module_name to remove from your environment the tools of the package.
  • use module list to know a each moment the list of modules//packages you've loaded in your environment.

In order to know which packages and version are available on the cluster, use the command module av. Without arguments this command will display the list of ALL available modulefiles (this list may be really important).
module av allows you to search for specific modulefiles using a word.

Warning this word correspond to the beginning of the module//package and is case sensitive case insensitive (modification performed on june 2014).

Example: module av bla will list all the modules whose name STARTS WITH bla.

tars:~ > module av bla ------------------------------------------------------------ /local/gensoft2/modules ------------------------------------------------------------ blast/2.2.21 blast+/2.2.29 blast2taxonomy/2.1(default) blat/35(default) blast/2.2.26(default) blast2seqids/1.3(default) blast2usa/1.2(default) blast+/2.2.28(default) blast2taxonomy/2.0 blastTaxoAnalysis/1.0(default)

To load a package//module, use the command module load module_name. Your environment will be modified and you will gain access to the tools from corresponding package.

Example:

module load blast/2.2.21

gives you access to the commands provided by the blast package, you're ready to use blastall, formatdb and other commands

At any time you can issue the command

module list

to display the modules that are currently loaded in your working environment. Example:

tars:~ > module list Currently Loaded Modulefiles: 1) blast/2.2.21 2) html4blast/1.7a 3) blast2seqids/1.3

You can see that the user has loaded the 3 following modules:

  • blast,
  • html4blast
  • blast2seqids.

The version of each loaded package is also displayed.

In order to bring your working environment to its initial state, use the command

module purge

This will unload ALL the modulefiles previously loaded.

For more details on module, its commands and possibilities see the advanced user guide