Get Set Up - statonlab/EPP_575_RNASeq_Workshop GitHub Wiki

Edit your OIT account

If you haven't already...

Navigate to https://setuplinux.utk.edu/, login. You may have to logout and log back in to get it to work. Make sure to click "Create Account" to ensure this works.

Activate the VPN

Get a shell on your laptop

• If you have an Apple
  • You have a built in terminal called Terminal
• If you have Windows 10
  • You have a built in terminal called Powershell
• Some other version of windows or Powershell not working?
  • Try mobaxterm

SSH

Time to try it out! At the command line prompt:

ssh [email protected]

Wow, you are connected to a supercomputer miles away! (Well, like 1/2 mile away)

The basics

Do you see a prompt? I hope so! (What is a prompt anyway?)

Our first command! "Print working directory" is equivalent to "where am I?". It is abbreviated as "pwd"

pwd

What's in this folder?

ls

What is the name of this computer?

hostname

We're going to explore these a lot more soon.

Get SWC files

Now we need to get the data for our lesson. We're going to use two new commands:

• wget = web get, i.e. download a file over the internet using its web address
• unzip = unzip a zipped file

wget https://swcarpentry.github.io/shell-novice/data/shell-lesson-data.zip

Check to make sure it is there:

ls

And lets decompress it:

unzip shell-lesson-data.zip

Access Spack system.

Within your home directory, update your .bash_profile to add the following:

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
	. ~/.bashrc
fi

# User specific environment and startup programs

export SPACK_ROOT=/pickett_shared/spack
PATH=$PATH:$HOME/bin:$SPACK_ROOT/bin
. $SPACK_ROOT/share/spack/setup-env.sh

exec newgrp statonutia