Lab internal

Getting started

Welcome to the lab! As you get started, you’ll need to sign up for two accounts:

• With the CS department account—ask Amy to send you instructions for this.
• An Office of Research Computing (ORC) account (click here). This is the compute cluster we use to analyze data.

ORC account setup

Getting an ORC account can take a few days. Once it is setup, ssh to the cluster at [netid]@ssh.rc.byu.edu. You can do this from a Linux or Mac terminal by executing ssh [netid]@ssh.rc.byu.edu. You need to setup 2-factor authentication with ORC for this to work. Check their website.

Once logged in, do the following to easily access lab software:

1. Put the following in ~/.profile:
   source $HOME/.bashrc
   (You can run nano ~/.profile to get a text editor. Another good text editor is vim, but this isn’t user friendly and requires time to get used to.)
2. Create a ~/.bashrc file:
   touch ~/.bashrc
3. Put the lab bin directory in your path (so that you can, e.g., execute ped-sim without specifying where that binary is). Add this to ~/.bashrc:
   export PATH="$PATH:/grphome/grp_hapidna/bin"
4. You can test that the above worked by executing:
   source ~/.bashrc
which ped-sim
   It should say /grphome/grp_hapidna/bin/ped-sim.

For the above to work, Amy needs to add you to the lab group on ORC. Send her a message if the above doesn’t work.