Using Docker (Post Workshop) - AlexsLemonade/2020-may-training GitHub Wiki

You will continue to have access to RStudio Server and the files in your home directory for 6 months following this workshop. We recognize there may be circumstances where you will need to process files locally. Running the same software that we use for training locally can be challenging, particularly for Windows users. (Some tools, like Salmon, are not supported on Windows.)

Docker is software that allows us to package a computing environment such that it can be fully reproduced between different computers and operating systems; it is sometimes referred to as a "lightweight virtual machine." We have put together a Docker image with the same software dependencies we use in training on the RStudio Server. The image we use will allow you to access an RStudio Server in your local container via your web browser.

You can find instructions for installing Docker on Mac OS or Windows 10 Pro here. Note: Windows Home has only recently become supported and requires different steps than what is linked above (Docker documentation).

Once you've installed Docker and Kitematic, you will need to pull the appropriate image using command line.

• In Mac, search for and open Terminal.
• In Windows, search for and open Command Prompt.

In your respective command line interface, copy and paste the following:

docker pull ccdl/training_rnaseq:2020-may-virtual

To run the container, change the <PASSWORD> in the line below to whatever you'd like.

docker run -e PASSWORD=<PASSWORD> -p 8787:8787 ccdl/training_rnaseq:2020-may-virtual

To work with files on your computer, you will need to set a local folder as your volume. It is important to note that anything that you save to the Docker container but not in a local folder is ephemeral - once you destroy the container, it disappears!

First, open Kitematic - you should see an image running. Docker assigns a random name to your container. In the example below: "stoic_lamport". If you don't see a container running, try quitting Kitematic and then opening it up again, or going to the toolbar > View > Refresh Container List.

Navigate to Settings > Volumes > Set local folder to the using the CHANGE button.

For Windows: After you set Volumes you will may see a message in the lower right corner of your screen that asks if you would like to 'Share it' with Docker. Click the Share it button; it will ask for your credentials. Enter your password and click OK.

Now, navigate to RStudio window.

• In a Windows or Mac in Kitematic, go to the Settings > Hostname/Ports tab and click on the blue lettering.
  
  
  
  

• Alternatively, for a Mac, you can navigate to the RStudio window by typing localhost:8787 in your web browser

Log into RStudio. The username will be rstudio and the password will be whatever you selected above. (Your password can also be accessed from the Settings > General panel in Kitematic if you forget!)

You should see a kitematic folder in your RStudio Files panel. When you click on it, you should see the contents of the local folder you connected above. Saving any files outside of the kitematic folder is strongly discouraged, as they will disappear once you've destroyed the container.