MODULES

Section: CCB Software Modules (7)
Updated:
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OVERVIEW

As well as the standard UNIX/Linux command line tools that you'd find on any other system, we've preinstalled over 200 bioinformatics programs for you to use. Many common programs are pre-loaded as soon as you log in, but some need to be loaded before you use them. We use the common module utility to do this.

module is a utility which is used to manage the working environment in preparation for running applications. By loading the module for a certain installed application, the environment variables that are relevant for that application are automatically defined or modified. At any time, a loaded module can also be unloaded, which allows you to dynamically choose which software you want available - including different versions of the same program.

LISTING AVAILABLE MODULES

You can display the modules available on CCB by typing:

$ module avail

You should see (something like) the following:

-------------- /package/environment-modules/modulefiles ---------------
alicevision/2.2.0               matlab/r2019b
allelecounter-castel/20181017   matlab/r2020a
amplimap/0.4.19                 meme/5.1.1
annovar/20180416                meme/5.3.0
annovar/20191024                meshroom/2019.2.0
aspera/3.9.8                    methpipe/4.1.1
aspera/3.9.9                    minimap2/2.17
atacqc/20170728                 miranda/3.3a
backspin/1.0(default)           mixcr/3.0.13
bam-readcount/20201113          moods/1.9.4.1
bamscale/0.0.5                  mosdepth/0.3.1
bamscale/1.0                    mpileup2readcounts/1.0

(output trimmed for space)

LOADING MODULES

You can load a module by typing:

$ module add module-name

For example:

$ module add bowtie

The above command will load the default version of an application. To load a particular version of an application use:

$ module add module-name/version

For example:

$ module add bowtie2/2.3.2

GETTING HELP WITH A MODULE

If you're not sure how to use the software provided by a module, you can use the built-in help. This will typically tell you website the program was downloaded from so that you can refer to the online manual, and occasionally has additional useful information.

$ module help juicebox
-------------------------------------------------------------------
Module Specific Help for /package/environment-modules/modulefiles/juicebox/1.9.8:

        Set up environment to use Juicebox
        Use 'juicebox-gui' for graphical interface and 'juicebox-clt' for command line tools
        Version built from github sources on 1.9.8

        Information re Juicebox may be found at
        http://www.aidenlab.org/juicebox/

-------------------------------------------------------------------

LISTING LOADED MODULES

Modules that are already loaded can be displayed with the command:

$ module list

UNLOADING MODULES

A module can be "unloaded" with the commands unload or rm , for example:

$ module unload bowtie

or:

$ module rm bowtie

REQUESTING ADDITIONAL SOFTWARE

If you'd like to use some software which isn't already available, please contact us so that we can discuss your requirements.

CAUTIONARY NOTICE ON CONDA AND VENVS

Many sources will tell you to use Conda or Python venvs to manage your software installations. Conda and Python are fine pieces of software and this is not a bad way to do software installation. However, please be aware that using venvs or Conda environments means inherently breaking compatibility with the systems software that we've installed for you. As such, we recommend that you do not attempt to use our modules whilst you have a venv or a Conda environment loaded, as it may cause both to break. Additionally, as both venvs and Conda environments are entirely installed in userland, we regret that, in many cases, we are unable to help with problems resulting from their use.

GETTING HELP

You can email the CCB team using the email address help@imm.ox.ac.uk. Using this address ensures your email is logged and assigned a tracking number, and will go to all the core team, which means the appropriate person or people will be able to pick it up.

COPYRIGHT

This text is copyright University of Oxford and MRC and may not be reproduced or redistributed without permission.

AUTHOR

Duncan Tooke <duncan.tooke@imm.ox.ac.uk>