.. _m3software:

Software on M3
**************

Modules
=======
M3 is a shared computing environment, and uses a modular system to manage software. 
This system provides an easy mechanism for updating your environment such as the ``PATH``, ``MANPATH``, 
and ``LD_LIBRARY_PATH`` environment variables, so that your environment uses the correct 
version of software and libraries installed on MASSIVE. This also prevents other users installing
software that may intefere with your personal software installs. 
You can find a list of our :ref:`installed modules here<m3availablemodules>`. 

There are some useful commands to know when using modules.

.. code-block:: bash
   
    # You can see what modules we have by using module avail
    module avail <software-name>

    # To use a module 
    module load <module-name>

    # You can see which modules are already loaded into your environment
    module list

    # To learn more about a particular module
    module show <module-name>

    # To stop using a module
    module unload <module-name>

    # To stop using all loaded modules
    module purge

    
Requesting an install
---------------------
If you require additional software please email help@massive.org.au with the following details:

    - software
    - version
    - URL for download
    - urgency
    - if there are any licensing restrictions we need to impose

Containers and Docker on M3
===========================
Many fields are beginning to distribute fully self contained pieces of software
in a container format with `Docker <https://www.docker.com/>`_. Unfortunately Docker is unsuited as a
container format for shared user systems, however it is relatively easy to
convert most Docker containers for scientific work flows to the `Singularity <https://sylabs.io/singularity/>`_
format. If you wish to run software based on a Docker container, please email
help@massive.org.au and let us know where we can obtain the container and we
will be happy to convert it for you.

Python and conda on M3
=======================
While there are Python modules installed on MASSIVE, you are unable to update or install your own Python packages into them.
This means it is usually best practice to use a conda or virtual environment to run Python on M3. 
Learn more about Python best practices at :ref:`Running Python and conda on M3 <pythonandconda>`.

Software for the Monash Bioinformatics Platform (MBP)
======================================================
The `Monash Bioinformatics Platform (MBP) <https://www.monash.edu/researchinfrastructure/bioinformatics>`_
maintains a software stack on M3. For more information, see the :ref:`bioinformaticsindex` community page.

.. include:: java-deprecation.rst