conda is a package management system that allows the installation of multiple versions of software through a virtual environment mechanism.

This system allows each cluster user to install and use the tools they need without the need of administrator rights.

Virtual environments

The tools you install through conda must be installed in a virtual environment that can be seen as a toolbox.

You can create as many virtual environments as you want, for example, to be able to use different versions of the same tool (each version in a different environment).

Creation

To create a virtual environment, use the conda create command like this:

conda create -n myenv

This command will create the virtual environment called myenv.

Activation

In order to use your virtual environment, you must activate it. To do this, use the following command:

conda activate myenv

Deactivation

When you no longer want to use the current virtual environment, just deactivate it:

conda deactivate myenv

Deletion

You can remove a virtual environment that is no longer needed by using the following command:

conda env remove -n myenv

Listing

Find a list of your virtual environments using the following command:

conda env list

By default, conda will store all of your virtual environments and the tools you want to install in the .conda folder located at the root of your home directory (/shared/home/<your_username>). They will thus be accessible on all the nodes of the compute cluster.

Clonage

You can clone an existing virtual environment to use as a starting point for a new virtual environment:

conda create -n myenv --clone snakemake

This command will create a new virtual environment myenv identical to the virtual environment snakemake available on the compute cluster.

Tools

Install tools

Once you have activated a personal virtual environment, you can install tools.

conda install git

The tools are made available by the conda community through numerous package repositories called channels.

The best known channels are:

• Default (https://anaconda.org) : Official conda channel (available by default)
• Bioconda (https://bioconda.github.io) : Repository of more than 3500 tools dedicated to bioinformatics
• Conda Forge (https://conda-forge.github.io) : Community channel

To install a tool from a particular channel, use the following command:

conda install -c bioconda snakemake

This command will install the snakemake package available on the bioconda repository.

You can create a virtual environment and install packages in one single command:

conda create -n myenv -c bioconda snakemake python==3.5

This command will create the virtual environment myenv and install the snakemake and python 3.5 packages.

List installed tools

The following command allows you to list all installed tools in the current virtual environment:

conda list

Remove a tool

To delete a tool, use the following command:

conda remove <tool>