A major aim of Biol7263 is to introduce you to commonly used and freely available tools for sequence alignment, assembly, comparison, and manipulation. We will primarily use these tools remotely on the OU supercomputing center for education and research system - OSCER. To access the OSCER we will need to setup a few programs on your computer.

For seminar, you will need to bring your own laptop computer with the following software setup:

Setup a terminal application

Windows systems

If you have a newer windows system (Win10 or greater) you can access this OSCER using Windows PowerShell. Look around, this should be installed on your system by default.

To log into the OSCER you simply type:

ssh [your username]@schooner.oscer.ou.edu

into the command line. You will then be prompted for you password. Note nothing appears at the cursor when you are entering you password.

If you prefer a terminal application with more features you can install MobaXterm details available here.

Mac systems

Similar to Windows, you can use the built-In terminal. You should be able to find this in your applications fold. Simply open it up and log into the OSCER by typing:

ssh [your username]@schooner.oscer.ou.edu

into the command line. You will then be prompted for you password. Note nothing appears at the cursor when you are entering you password.

The nice thing about Macs is that they are UNIX-based and so all of the commands we will learn for navigating the OSCER system can be used locally on your machine!

File transfer

We will submit command to the OSCER through the terminal, but we will also need to load data and script files. There are several options to do this, I will use and suggest WInScp (for windows) and FileZilla (on Mac). Please select one and install it ahead of class.

Text/Script editor

I find it easiest to write and edit scripts locally in a standalone text editor and then upload to the OSCER. There are many options, but the one I am most familiar with and will use in class is Notepad++. This resembles the basic windows notepad, but has a range of additional functions that are helpful to manage code and other text files. If you find another option you prefer, feel free to use that one.

Important Note for Windows users Windows programs will often add hidden end of line characters that cause lots of trouble. When saving a file for upload to OSCER be sure to convert the line ends to unix. In Notepad++ this can be done here:

Install R

Follow this link: http://lib.stat.cmu.edu/R/CRAN/ and choose your platform (Windows, Mac, or Linux). The latest R version is: R 4.4.1 “Race For Your Life”.

Install R studio

Go here: https://rstudio.com/products/rstudio/download/#download

If you have an old Mac : here is a list of older versions - https://rstudio.com/products/rstudio/older-versions/

Install R markdown

To setup Markdown in R, open Rstudio and then open a markdown file as shown below

This should bring up a dialog asking if you want to install the required packages. Click yes. Once installed a dialog box should pop up asking you to name your markdown file. Go ahead close out of this. The required packages should now be installed.

Install Git

For this class we will implement and manage version control with git through R. To do this you will need git software. Please download and install git from git-scm.com.

Setup a github account

We will use GitHub to archive and share assignments and class projects. If you do not yet have a github account, please sign up for a free, public account.