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 different appearance of the local shell
2. Briefly explore your local files
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. Briefly explore remote files
6. Use exit to log off, return to local shell

# 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
# Briefly explore remote files
ls -l
# Log off, return to local shell
exit

Click here for demonstration of local (git-bash on Windows) vs remote (AWS)

1.4 Orientation exercise

Note: We will provide additional time during this exercise to ensure that everyone is prepared to move forward.

Orientation exercise:

1. Log in (or confirm logged in) to aws instance
2. Ensure in home directory with cd
3. Use ls to view references
4. Use ls to view input fastq files
5. Use mkdir to create a folder for our analysis

# Log in to aws remote
ssh <username>@bfx-workshop01.med.umich.edu
# Ensure we are in home directory
cd
# View our references
ls ~/data/refs
# View our input fastq files
ls ~/data/reads
# Create a folder for our analysis
mkdir ~/analysis