.. _docs_checklist:

GenPipes Check List
===================

Before you begin using GenPipes for the first time, it would be useful to quickly go over the basic requirements of using GenPipes.  This checklist is created to help you get started with GenPipes quickly and get your bearings correct before you embark upon genomic analysis with GenPipes.

.. include:: /common/new_gp_wizard.txt

.. |check-img| image:: /img/checkmark.png
   :scale: 5%
   :align: top

Skill sets and domain know-how
------------------------------

The following table lists some of the skill sets, technologies and know-how that a GenPipes user is expected to have.

+--------------+-------------------------------------------------------------------------------------------------+
|              |                     Requirements                                                                |
+==============+=================================================================================================+
| |check-img|  | `High Performance Computing (HPC) for genomics`_ - environment and software modules used        |
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | `Cluster Computing`_, `Cloud environment`_ for genomics                                         |
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | `DRAC`_ formerly Compute Canada HPC infrastructure `usage account`_ and familiarity             |
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | Use of shared, distributed File Systems such as `CVMFS`_                                        |
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | HPC Schedulers such as `PBS`_, `Slurm`_                                                         |
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | Bioinformatics Software :ref:`Dependencies<software dependencies>` (Local/Pre-installed on CCDB)|
+--------------+-------------------------------------------------------------------------------------------------+
| |check-img|  | GenPipes :ref:`Basic Concepts<docs_what_is_genpipes>` - Pipelines, steps etc.                   |
+--------------+-------------------------------------------------------------------------------------------------+

Pre-requisites for running GenPipes
------------------------------------

Besides the skills and technologies listed above, you need powerful hardware and some pre-installed software modules before you can run GenPipes.  For a complete list, please refer to :ref:`docs_pre_req_chklist` for details.

.. The following are html links used in the content above

.. _High Performance Computing (HPC) for genomics: https://people.eecs.berkeley.edu/~yelick/talks/data/GenomicsHPC-BERGenomicsPI18.pdf
.. _Cluster Computing: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655901/
.. _Cloud environment: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452449/
.. _usage account: https://ccdb.alliancecan.ca/account_application
.. _CVMFS: https://cvmfs.readthedocs.io/en/latest/
.. _PBS: https://www.openpbs.org 
.. _Slurm: https://slurm.schedmd.com/tutorials.html
.. _Drac: https://alliancecan.ca/en