Day 1 - Module 01: Warming up

1 Warming Up

In this module, we will:

• cover basic materials needed
• familiarize ourselves with remote computing
• prepare for later modules

1.1 Building Blocks

1.2 Example Files Exercise:

1. Download the zipped archive from the slack channel
2. Locate, move (if desired), and unzip it
3. Remember how to access these files

1.3 Local vs Remote Exercise:

1. Become familiar with the appearance of the local shell
2. Briefly explore your local files (optional)
3. Log in to the aws instance with ssh <username>@bfx-workshop01.med.umich.edu
4. Become familiar with appearance of the remote shell
5. Use ls to view references
6. Use ls to view input fastq files
7. Use mkdir to create a folder for our analysis

# Familiarize with local shell appearance
# Briefly explore your local files
ls -l
# Log in to the aws instance via ssh
ssh <username>@bfx-workshop01.med.umich.edu
# Familiarize yourself with differences between local and remote shell
# View our references
ls ~/RSD_Shell/refs
# View our input fastq files
ls ~/RSD_Shell/reads
# Create a folder for our analysis
mkdir ~/RSD_Shell/analysis

Click here for demonstration comparing local Windows command prompt vs remote (AWS)