GEMSCAN_on_Biowulf_00_preworkshop_setup

Pre-Workshop set up

Setup for workshop (please do this before the workshop)

This workshop is intended for running the GEMSCAN small variant ensemble caller on Biowulf. Before the workshop, please obtain an account on Biowulf and familiarize yourself with the Biowulf system. The user guide here should be quite helpful.
The batch system on Biowulf is Slurm so the tutorial is largely applicable to other Slurm systems as well.

Software needed for the workshop

We expect that you have your own computer connected to the Internet to follow along, therefore you will need to obtain a terminal program on your computer. The instruction below covers Windows, OS X and Linux.

Windows

There are several choices. If you just want to use a terminal to connect to the Biowulf cluster, you could use Putty. Alternatively, NoMachine provides you with a desktop GUI. Download Putty here Download NoMachine here

OS X

The pre-installed Terminal program or iTerm2 or Hyper would be fine or if you prefer to have a desktop GUI, there's an OS X version for NoMachine provided by the NIH HPC team [here]https://hpc.nih.gov/docs/nx.html)

Linux

The default Terminal program available in most Linux distros would be fine

Connecting to Biowulf

In your terminal program, type

ssh <yourUserName>@biowulf.nih.gov

For more details, read the Biowulf guide here