OSCER and BASH, BASH and OSCER

Author

Eleana Cabello

Published

June 2, 2025

Setting the Stage

Terminal - A text-based user interface that allows users to interact with a computer by typing commands
Directory - A folder location in your computer
Working Directory - The current directory a user is in
Path - Directions to a folder or file
Command - BASH command to accomplish a task i.e. creating file, removing file, etc.
Command Flag - Modifications to a command to consider

Logging into OSCER Guest Account

Good news! There is nothing you need to do to setup an account. A guest account has already been made for you by us for FREE!

Steps to Log In

Gather you log in information, username and password.
Find the terminal on your computer.

Type the following command to access you OSCER account

ssh USERNAME@sooner.oscer.ou.edu #Replace USERNAME with your guest username

It will ask for your password, start typing it. It will not appear on your screen do not be alarmed this is normal. Just make sure to enter it correctly then hit enter.
You’ve logged into your account!

Working on OSCER’s HPC System

Your computer is set up in a way where everything is together. Files, programs, and hardware are physically put into one place whether it be a tower or laptop. These system also typically use graphic user interfaces (GUI) like a window for Word or web-based applications. In this course we will primarily not be using these methods of communication with your computer. Instead we will be using things like the terminal, progrmaming scripts, and simple text editors to complete computational tasks.

The OU Supercomputing Center for Education and Research (OSCER) provides the OU, OUHS, and other Oklahoma institutions with High Performance Computing (HPC) infrastructure.

HPC system allow for multiple jobs to be run on several processors in a multi-processor enviroment. This is also known as parallel processing. A simple way to put it, it allows for multiple people to submit jobs/processes at the same time. It also means you can submit several jobs at a time and not have to wait for the “computer” to free up after each task.

Why do we need parallel processing? Think about it as a queue you are in, waiting to submit your job to do on a computer. Your job takes about 5 hours to complete. The person infront of you takes about equal or more and so does the next person infront of them. Whether you are using a computationally heavy program or just have hundreds of samples to process Without parellel processing you will have to wait there for days as one by one gets done in front of you. HPC parallel processing allows for multiple queues for computationally heavy jobs to get done in a faster amount of time.

The figure above shows the overview of OSCER’s HPC structure. In a traditional computer you files system is very much merged with your processing system. Since an HPC system has hundreds even thousands of users, this is not possible to do with an HPC and would likely defeat its purpose. Instead you file system “Home” is seperate from your processing system “Compute Nodes” in this structure. Programs are also seperated from your “Home”.

OSCER and HPC Resources

BASH Programming

The following commands will help you navigate through your OSCER account and submit jobs.

Navigating Directories

pwd       # Print wokring directory

ls        # List contents in a directory
ls -lh    # List contents in a directory in a list format and human read able sizes

tree      # List directory and file tree

cd SOME_DIR     # Change working directory to the entered directory 
cd ..           # Change working directory to parent directory of current directory
cd ~            # Change working directory to home

Creating, Moving, and Deleting Directories

mkdir SOME_DIR    # Create directory

rmdir SOME_DIR    # Remove Directory
rm -r SOME_DIR    # Remove Directory

mv ONE_DIR TWO_DIR # Move directory to new directory

Creating, Deleting, Copying, and Moving Files

touch SOME_FILE.txt                   # Create new file
touch SOME_FILE.txt SOME_FILE.txt     # Create several new files

rm foo.txt                        # Remove file

cp SOME_FILE.txt SOME_FILE.txt    # Copy file to new directory
mv SOME_FILE.txt SOME_FILE.txt    # Move file to new directory

Piping

CMD1 SOME_FILE.txt | CMD2         # Structure

ls SOME_DIR | grep "R1"           # Example

Standard Output

echo "some string"                # Print to screen

CMD SOME_FILE.txt > NEW_FILE.txt            # Overwrite file with output
CMD SOME_FILE.txt >> ADD_TO_EXISTING.txt    # Take output and add output to existing content in file

CMD SOME_FILE.txt 1> stdout.txt           # Redirect the standard output to a file
CMD SOME_FILE.txt 2> stderror.txt        # Redirect the standard error output to a file

File Editing

nano                    # Opens text editor to create new file
nano file.txt            # Opens file in text editor

Pattern Searching

grep "some-string" SOME_FILE.txt    # Grabs lines in file that contain the string pattern

Batch Scripting and Programs on OSCER

Working on an HPC means we have to communicate with it using its language which is Bash and Bash scripting.

To use a bioinformatics program we will need to submit jobs through a Bash script. In a sense you will have to anticipate what will need to be done in this script. For example if you want to store your results in a seperate folder than you are working in you will need to create that folder and set the path for those results. Below is an example of what each script will need at the beginning:

#!/bin/bash
#SBATCH --partition=ircfhp
#SBATCH --nodelist=c923
#SBATCH --container=el9hw
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=10
#SBATCH --mem=30G
#SBATCH --chdir=/ecabello
#SBATCH --output=qc_%A_%a_stdout.txt
#SBATCH --error=qc_%A_%a_stderr.txt
#SBATCH --mail-user=eleana-cabello@ouhsc.edu
#SBATCH --mail-type=ALL


#==============================================================================
# BASH Strict mode (i.e. "fail fast" to reduce hard-to-find bugs)
set -e          # EXIT the script if any command returns non-zero exit status.
set -E          # Make ERR trapping work inside functions too.
set -u          # Variables must be pre-defined before using them.
set -o pipefail # If a pipe fails, returns the error code for the failed pipe
                #  even if it isn't the last command in a series of pipes.
#==============================================================================

module load fastqc
module load multiqc

Lecture 1 Assignment

Lecture 1 Homework