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Using Mamba (conda) for the first time

First get an interactive session: 

ssh username@alma.icr.ac.uk
srun --pty -t 12:00:00 -p interactive bash

In order to use conda, users should add the EasyBuild modules to their user path and load the Mamba module:

module use /opt/software/easybuild/modules/all
module load Mamba

You can check that the module has been loaded successfully by running module list, which should return the output:

Currently Loaded Modules:
  1) slurm-21.08.5   2) Mamba/23.1.0-0

In addition to any other modules you may have already loaded. You can further check that the mamba and conda commands are now available for you to use, via mamba --version, which should return the output:

mamba 1.4.0
conda 23.1.0

2. Initialize your shell

After the module has been loaded, you should now initialize your shell. The easiest way to achieve this, is to run

mamba init

This should generate the output:

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.4.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

no change     /opt/software/easybuild/software/Mamba/23.1.0-0/condabin/conda
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/bin/conda
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/bin/conda-env
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/bin/activate
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/bin/deactivate
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/etc/profile.d/conda.sh
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/etc/fish/conf.d/conda.fish
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/shell/condabin/Conda.psm1
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/shell/condabin/conda-hook.ps1
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/lib/python3.10/site-packages/xontrib/conda.xsh
no change     /opt/software/easybuild/software/Mamba/23.1.0-0/etc/profile.d/conda.csh
modified      /home/<username>/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

Added mamba to /home/<username>/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

It is important that we pay attention to the last part of this output: Close your Alma terminal and open it up again. You can litteraly close and open your Alma terminal, or alternatively run:

$source ~/.bashrc

3. Using conda post-initialization

After you have started a fresh terminal session, you do not need to follow the previous steps again. Check that you can run

mamba --version

which as before, should now return:

mamba 1.4.0
conda 23.1.0

You should now be ready to use conda.

4. Adding preloaded path for Alma

Alma has some preloaded environments that you can use if you are looking to just use a single tool (you can't add to the environments). You can add these to your path by running:

conda config --append envs_dirs /opt/software/applications/anaconda/3/envs/

You can then see that you have these environments by running:

conda info --envs

And activate them by running, for example:

conda activate star2.7.6a