Gubbins
-------
Genealogies Unbiased By recomBinations In Nucleotide Sequences - Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

`Gubbins <https://github.com/nickjcroucher/gubbins>`_ is made available on the cluster as a shared :doc:`Apptainer <apptainer>` container image. 

You can use the :code:`apptainer/gubbins` module which will add convenient aliases to Gubbins scripts, such as  :code:`run_gubbins.py`, which will run within the container.

To use any of the aliases in a non-interactive/SLURM batch script, add the following in your script before using the alias: :code:`shopt -s expand_aliases`.

See the `Gubbins manual <https://github.com/nickjcroucher/gubbins/blob/master/docs/gubbins_manual.md>`_ for usage information. Example:

.. code-block:: bash

    module load apptainer/gubbins
    # The following is required to use aliases in a non-interactive/SLURM batch script:
    shopt -s expand_aliases
    run_gubbins.py <FASTA alignment>