LiCSAR Wiki (from gitlab)
=========================

General LiCSAR related information
----------------------------------

1. `COMET portals and related links <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/licsar_links>`_
2. `LiCSAR related tools <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/licsar_tools>`_
3. `LiCSAR related talks <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/licsar_talks>`_


New User
--------

1. Register yourself at CEMS/JASMIN and its relevant services: `jasmin_setup <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/new_user/jasmin_setup>`_

2. Learn the first steps about CEMS/JASMIN services (including ssh settings etc.): `cems_quick_start <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/new_user/cems_quick_start>`_

3. Set yourself to licsar modules and learn to use licsar_framebatch: `licsar_settings <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/new_user/licsar_settings>`_

4. Setting for LiCSAR environment on Leeds Uni servers: `leeds_uni_setup <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/licsar_settings_leeds>`_


Getting users into details
--------------------------

1. Tutorial related to NLA: `nla <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/nla>`_
2. CEDA JASMIN (previously CEMS) processing strategy (processing queues etc.): `lotus queues <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/lotus_queues>`_
3. Other detail notes: `other <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/notes>`_ - including instructions for data copying from CEMS etc.

Use the LiCSAR codes
--------------------

#. Tutorial to use licsar_framebatch procedure:  

   `automatic licsar_framebatch <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/licsar_framebatch>`_ - main functionality, allowing fast and easy processing of selected frame  

   `manual/detailed licsar_framebatch <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/licsar_framebatch_manual>`_  

#. `customizing the processing <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/tutorials/licsar_custom>`_ - e.g. custom snaphu parameters etc.

#. Setting up `LiCSAR environment at Leeds Uni servers <https://gitlab.com/comet_licsar/licsar_documentation/-/wikis/licsar_settings_leeds>`_ (not JASMIN)


Processing at JASMIN
--------------------

LiCSAR at JASMIN notebooks
^^^^^^^^^^^^^^^^^^^^^^^^^^

Although we use primarily JASMIN as in materials above (i.e. ssh in terminal), one can also access `JASMIN Jupyter Notebook service <https://notebooks.jasmin.ac.uk>`_ .
And if you run a simple script in sci server terminal: `install_mamba_jupy.sh`, you will then be able to connect to mambalics environment that includes LiCSAR testing codes.
Consider this message a LiCSAR Easter Egg..

Note: while you will have access to /gws folders for reading, you will NOT have access to /scratch disks and you will have write rights only to your home directory.