===================
Account Setup Guide
===================

While it is possible to Validate using your own hardware, you'll
benefit from greatly enhanced speed and reliability using high-speed
compute resources freely-available from the open-source science
community. You'll need to set up accounts with Cyverse_, the Texas
Advanced Computing Center (TACC_), and Extreme Science & Engineering
Discovery Environment (XSEDE_) to gain the most benefit from these
tutorials. If you're working in an academic laboratory, you should
have little trouble registering for accounts and allocations available
to users with a .edu email address. Bear in mind that large
allocations may require approval for a specific research need.

.. _Cyverse: http://www.cyverse.org/
.. _TACC: https://www.tacc.utexas.edu/
.. _XSEDE: https://www.xsede.org/

Cyverse
~~~~~~~

Register at https://user.cyverse.org/. This portal will be your
central access point for Atmosphere and the Discovery Environment, and
provides some forums for community and support.

- Your default Data Store allocation is 100GB, which can be upgraded
  upon request to up to 1TB. For more information see
  http://www.cyverse.org/data-store.

- To gain access to Atmosphere images, which can be a convenient way
  to quickly get started in a linux environment pre-configured for
  GWAS analysis, you'll need to request access_ through your cyverse
  dashboard.

.. _access: http://www.cyverse.org/learning-center/manage-account#AddAppsServices

TACC
~~~~

These guides refer to running the Validate workflow on the Stampede
supercomputer at the TACC. You'll need to make an account at
https://portal.tacc.utexas.edu/ to get started. Unless you are a
professor or in charge of a collaborative project at your
company/institution, simply list the PI option near the end of the
application as *Ineligible*. After you've created your account, you'll need to configure two-factor authentication back at the user portal before you can log on to TACC machines.


XSEDE
~~~~~

Extreme Science & Engineering Discover Environment represents a
collection of advanced digital services for scientific
collaboration. Your account with them grants you access to the Agave
API for job submission and data management, and allows you to run jobs
on Stampede using "iPlant-collabs" project allocation.

- Register for an account following the steps at
  https://www.xsede.org/using-xsede
- To use Agave, request an allocation following the instructions at
  https://portal.xsede.org/allocation-request-steps
  

If you are a staff member at the iPlant Collaborative, send a message
to support@iplantcollaborative.org to request access to the
"iPlant-Collabs" allocation. Getting access may take a day or two, but
you will know for sure upon trying out Stampede for yourself. **Note
that you will not immediately receive a notification upon getting
access. The only way to know for sure is to try it out!**

==================
Accessing Stampede
==================

To access Stampede, you may use a number of different SSH clients,
depending on your operating system::
  
  localhost$ ssh taccuserid@stampede.tacc.utexas.edu


For Windows:
~~~~~~~~~~~~

SSH support is built into PowerShell for Windows 10.

For the technically curious or advanced, `Cygwin
<https://www.cygwin.com/>`_ is an open-source project to bring a
Unix-like environment to windows. While the initial installation
options may be overwhelming, all you need are the ssh tools to use the
shell to access Stampede. You may also quickly get an Ubuntu image up
and running through Atmosphere once you've set up your Cyverse
account.

* `PuTTY <http://www.putty.org/>`_: a no-frills Unix-esque SSH client
* `WinSCP <http://winscp.net/eng/index.php>`_: A more user-friendly
  interface similar to Windows Explorer. Allows integration with PuTTY
  and drag-and-drop transfer of files from local drive to remote
  computer.
 
  
For Mac:
~~~~~~~~

* Terminal: ssh is built into Mac OS. For extensive use many prefer
  `iTerm2 <https://www.iterm2.com/>`_.
* `Cyberduck <https://cyberduck.io/>`_

For Unix/Linux:
~~~~~~~~~~~~~~~

* Terminal: The standard Unix terminal may be used to access Stampede
  through the *ssh* command.