Welcome to the Cloud CIX user guide!
====================================

This website is a user manual for beginners getting setup with the Cloud CIX platform, taking you through creating a virtual machine and installing basic unix tools to begin planning your own bioinformatics workflows. This website does not offer assistance in setting up an account, which is handled by the admin team at Cloud CIX.

.. note::

   If any of the URLs or code blocks no longer work please open an issue at `https://github.com/BarryDigby/Cloud_CIX/issues <https://github.com/BarryDigby/Cloud_CIX/issues>`_ describing both the error and location of the error. Please refrain from posting technical questions to the issue tracker.

List of contents
*******************************

- :doc:`Creating a virtual machine </man_pages/virtual_machine>`

- :doc:`Logging in to your virtual machine </man_pages/accessing_vm>`

- :doc:`Installing basics for your virtual machine </man_pages/install_basics_vm>`

- :doc:`Tips for customising your terminal <man_pages/bashrc>`

- :doc:`Installing package managers </man_pages/package_managers>`

- :doc:`Installing container clients </man_pages/containers>`

- :doc:`Installing tools & creating projects </man_pages/install_tools>`

- :doc:`Using your virtual machine to host Posit tools </man_pages/hosting_rshiny_app>`

- :doc:`Adding content to this guide </man_pages/contributing>`


.. toctree::
   :maxdepth: 3
   :caption: Cloud CIX Virtual Machine
   :hidden:

   /man_pages/virtual_machine
   /man_pages/accessing_vm
   /man_pages/install_basics_vm
   /man_pages/bashrc

.. toctree::
   :maxdepth: 3
   :caption: NUIG users
   :hidden:

   /man_pages/nuig

.. toctree::
   :maxdepth: 3
   :caption: Install Package managers
   :hidden:

   /man_pages/package_managers

.. toctree::
   :maxdepth: 3
   :caption: Install Container Clients
   :hidden:

   /man_pages/containers

.. toctree::
   :maxdepth: 3
   :caption: Installing Tools
   :hidden:

   /man_pages/install_tools

.. toctree::
   :maxdepth: 3
   :caption: Hosting Posit tools
   :hidden:

   /man_pages/hosting_rshiny_app
   /man_pages/rstudio_server

.. toctree::
   :maxdepth: 3
   :caption: Miscellaneous
   :hidden:

   /man_pages/contributing