Lab 1 - Unix and Multiple Sequence Alignment

In this lab we will review some basic

Before the class:

1) Learn/review some basic Unix commands before the class.

• If you are new to Unix, go through tutorials one and two here. Note, that you can run unix in your browser! (e.g., here)
• It would be very useful to know basics of the vi(m) editor. I prepared a tutorial for you.

2) Install Git/Git Bash

• On Mac: Check if Git is installed by typing git in your terminal. Follow the instructions if Git is not installed.
• On Windows: Download the most recent version of the program from here.
• To learn more about git go through the following (optional) tutorial

3) Get a GitHub User Account

Create a user account on GitHub if you don’t have one already. Be sure to choose a user ID that you are happy using for the rest of your professional career.

4) Install the VPN software if you are working off campus.

Go the link and follow the instructions.

In class:

Connect to the HPC-class server (now part of Nova)

Open the Terminal application on Mac/Linux or GitBash on Windows. Type ssh <ISU NetID>@nova.its.iastate.edu, where netID is your university username.

Imporant: Accounts on Nova Cluster require the use of Google Authenticator. The Google Authenticator provides a six digit one-time password users must provide in addition to their username and password to log into Nova Cluster.

If you don’t have Google Authenticator installed, follow the instructions on the HPC Nova website.

At the first attempt to login to Nova a GA account will be created for the user, and the email with the instructions will be sent to @iastate.edu.

Git SetUp on Nova

Linking your Nova account to GitHub

We need to do a few things in your home directory. Just follow the instructions and don’t worry about the details at the moment.

In your home directory, type ssh-keygen and press enter to confirm the name of the file. If you get a message that the file already exist, don’t overwrite it.

Type cat ~/.ssh/id_rsa.pub and copy your public ssh key. Go to your GitHub account and click on your picture in the upper right corner. Select “Settings”. Choose “SSH and GPG keys” under “Personal settings”. If you don’t have it already, enter a new SSH key for hpc-class. Paste your public ssh key there. Click on “Add your SSH key.

A few configuration steps

Because Git is meant to help with collaborative editing of files, you need to tell Git who you are and what your email address is. To do this, use: git config --global user.name "Sewall Wright"
git config --global user.email "swright@adaptivelandscape.org"
Make sure to use your own name and email, or course!

Another useful Git setting to enable now is terminal colors: git config --global color.ui true

Cloning a repository

Go to the EEOB563-Spring2023 repository and copy its SSH address under Clone or Download.

Run the following command in your home directory on HPC-class:
git clone <repository address>

Updating a repository

To update a Git repository, enter the following command:
git pull

UNIX

Unix exercise

Multiple Sequence Alignment

MSA exercise

A useful trick

It is rather tedious to type the whole ssh <netID>@hpc-class.its.iastate.edu command and to enter the password every time you connect to HPC-class. So here is a trick for you! On your own laptop computer create an .ssh directory by typing ssh-keygen in your home directory. Use the following command to paste info into the config file (which may not yet exist) in .ssh directory:

echo "host hpc-class
HostName hpc-class.its.iastate.edu
User dlavrov" >> ~/.ssh/config

Now enter the following command: ssh-copy-id -i ~/.ssh/id_rsa.pub <your_username>@hpc-class.its.iastate.edu. It will ask you for your hpc-class password.

Next time you connect to HPC-class, just enter ssh hpc-class. You won’t need either to type anything else or to enter your password! Enjoy!

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