Using genairics on UGent HPC (instructions for Mac users)
---------------------------------------------------------

Request account
===============

Open a terminal: make the key combination `CMD-space` and type
`terminal`, click on `Terminal` with the black 'terminal' icon.

In the terminal copy paste the following line:

    ssh-keygen

Press enter, and press enter for every question (in total 4x `enter`).
Now you are ready to go and request a vsc account, by clicking on the
following link: `https://account.vscentrum.be/ <https://account.vscentrum.be/>`_.

.. image:: /images/vsc/request_account_startscreen.png

Once you are logged in, go to the `Edit Account` section.

.. image:: /images/vsc/vsc_edit_account.png

At the bottom of the screen you can upload the key that you made
earlier with `ssh-keygen`.

.. image:: /images/vsc/vsc_edit_account.png
.. image:: /images/vsc/vsc_upload_key2.png

To reach the `.ssh` folder where you can find the file to select
(`id_rsa.pub`) type `CMD-SHIFT-G` and fill in `~/.ssh`.

When you have uploaded the key, you should receive a mail that your
account will be activated. You should also be notified of your unique
vsc id number `vscXXXX`. In the following, whenever `vscXXXX` is
written, replace it with your own number.

Prepare your work environment
=============================

Open a terminal, or continue to work in one already opened. And
execute the following lines one by one.

.. code-block:: sh

   ssh vscXXX@gengar.ugent.be
   wget -O ~/.bashrc https://raw.githubusercontent.com/dicaso/genairics/master/genairics/scripts/gax_bash_vsc.sh
   source ~/.bashrc
   mkdir -p $GAX_RESOURCES/repos $GAX_DATADIR $GAX_RESULTSDIR
   module load pandas
   pip install --user genairics
   genairics -h

If all went well, the last line gives you the genairics help
output. You are now ready to start and use genairics.

GAX dependencies
================

If you are installing genairics as part of a personal account on the
hpc, or your vo group has not yet been setup to run genairics, the
following step is also required in order to use genairics.

In your ssh session, start up a console with `genairics console` and execute the following line:

.. code-block:: python

		InstallDependencies()

Get your BASESPACE_API_TOKEN accessToken
========================================

If you want to run analyses starting from an Illumina Basespace
project you need to have an accessToken to be able to download your
data in the pipelines. Follow the steps 1-5 from this link:

`https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/ <https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/>`_

.. code-block:: sh

		emacs ~/.BASESPACE_API #Store your accessToke here, instead of emacs use any editor you like
		chmod 600 ~/.BASESPACE_API #For security, only rw access for your user

Optional: ssh config
====================

TODO: (sshconfig -> ssh vsc)


Submit job to different cluster
===============================

Example submit on golett.

1. Find out server name

.. code-block:: sh

		module swap cluster/golett
		qstat -q
		QSERVER=master19.golett.gent.vsc
		module swap cluster/delcatty

2. Submit job with queue argument --cluster-Q

    genairics --job-launcher qsub --cluster-Q @master19.golett.gent.vsc --remote-host vsc ATACseq NSQ_Run240