danekennedy / OMICS

Drexel Medicine OMICS course

Drexel Medicine OMICS

Week 1 Summary: Intro to JupyterHub, Linux and GitHub

1. Log in to Drexel Medicine JupyterHub
2. Open a terminal window in JupyterHub
3. Make a directory to store your projects (w/Linux commands)
4. Commit (save vertion) and backup your project (w/GitHub)
5. Lab instructions

Weekly Details

Week 1 Details: Intro to JupyterHub, Linux and GitHub

1. Log in to Drexel Medicine JupyterHub

• Install Drexel Medicine VPN: https://drexel.edu/it/help/a-z/VPN/
• Login to the Drexel Medicine:

2. Open a terminal window on JupyterHub

2a. Open JupyterHub

http://10.11.19.24/

2b. Open a terminal window

In web browser, from JupyterLab menu:

File -> New -> Terminal

3. Make a directory to store your projects (w/Linux commands):

In the terminal window that you just opened, type each command and press the [Enter] button:

• Show the name of your home directory (pwd)
• Show contents of your home directory (ls)
• Make a new directory to store your projects (mkdir repos)
• Change to your new directory (cd repos)

4. Save and backup your projects (w/GitHub)

• Create an account on https://github.com
• Copy the Drexel Medicine OMICS project to your GitHub account (fork)
• Download a copy to your PC (git clone https://github.com/<your_profile>/OMICS)

5. Week 1 Lab Instructions

5a. Create a batch file, week01_lab.sh which contains all commands from step 2:

nano is a command-line text editor.
But you can use your favorite editor:

• nano week01_lab.sh
• vim week01_lab.sh
• emacs week01_lab.sh

$ cd ~/repos/OMICS
$ nanno week01_lab.sh

5b. Commit week01_lab.sh to your local disk:

$ cd ~/repos/OMICS
$ git add week01_lab.sh
$ git commit week01_lab.sh -m 'Adding lab batch file'

5c. Backup your work to GitHub:

$ git remote -v
origin 	https://github.com/[studentrepo]/OMICS.git (fetch)
origin 	https://github.com/[studentrepo]/OMICS.git (push)
$ git branch
* main
$ git push origin main

5d. Run your batch file:

source week01_lab.sh | tee week01_lab.txt

Copyright (C) 2023-present, Drexel Medicine. All rights reserved