Software
========

.. |rstudio_url| replace:: https://klima.uod.otago.ac.nz

.. |hostname| replace:: klima.uod.otago.ac.nz


.. include:: /common/spack/packages/conda.rst


GLOBE Claritas
+++++++++++++
To start the Claritas GUI (in an :doc:`Apptainer </common/containers/apptainer>` container):

.. code-block:: bash

  claritas-7.4.1.sif

.. include:: /common/matlab.rst
MATLAB with the relevant toolboxes on |hostname| is also available as an :doc:`Apptainer </common/containers/apptainer>` container image, for a more self-contained and portable workflow.

.. code-block:: bash

    MATLAB-R2023a-klima-0.1.sif

.. include:: /common/containers/apps/ncstat.rst

.. include:: /common/spack/packages/nco.rst

Jupyter
+++++++
JupyterHub is available at: https://klima.uod.otago.ac.nz/jupyter

Use your University credentials to login.

Jupyter can also be started from within a customised environment (conda, Spack, etc).

In an X session (FastX, X2Go), open a terminal window, and activate the respective environent.

.. code-block:: bash
    
    conda activate foo
    conda install ipykernel
    jupyter notebook

Your Jupyter Notebook instance should open in a browser window. If not, take note of the URL, eg http://localhost:8888/?token=...
and copy-paste this in the browser within your X2Go session.

Then when creating a new notebook, make sure to select the conda environment in the 'kernel' dropdown.


OpenGrADS
+++++++++
OpenGrADS is distributed as an :doc:`Apptainer </common/containers/apptainer>` container. 
To start the container, run:

.. code-block:: bash

  opengrads_v2.2.1.oga.1.sif 

The prompt will change to :code:`Apptainer>`; You're now in a shell within the container, where you can run the GrADs binaries.
e.g.: :code:`grads`


.. include:: /common/spack/packages/python.rst

.. include:: /common/spack/packages/r.rst

.. include:: /common/rstudio.rst
For more flexibility, R Studio can also be launched :doc:`as a container </common/containers/apps/rstudio.rst>`.