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Docker Container Set Up - from Internet

If you have successfully installed Docker, and have copied the files from the flash drive you are now ready for the last part of set up: setting up your Docker container.

Setting up your Docker container as described by these steps, will provide you with all the software and packages you need for this workshop.

  1. 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:2019-philly
  1. 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:2019-philly
  1. 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.

  1. Settings > Volumes > Set local folder to training-modules that was transferred from the flash drive, using the CHANGE button. Folder

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:
Folder
Enter your password and click OK.

  1. Navigate to RStudio window.

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

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

  1. Log into RStudio. The username will be 'rstudio' and the password will be whatever you selected above (can also be accessed from the Settings > General panel).

  2. You should see a kitematic/ folder in your RStudio Files panel. Click on it.

  3. To test that everything is set up, copy and paste the follow command in the R Studio Console window.

source("kitematic/ready_script.R")

Ready

  1. Click Enter. You should receive an indication that you are successfully set up. Keep this indicator handy for the instructors and helpers as they come around to check.

If Kitematic doesn't work:

If all else fails and Kitematic is not working for you, go to your Terminal or Command Prompt (for Mac or Windows respectively) and type in the following, but replace <PATH_TO_TRAINING_FOLDERS> with the absolute path to training-modules that was transferred from the flash drive.

docker run -it --rm --mount type=volume,dst=/home/rstudio/kitematic,volume-driver=local,volume-opt=type=none,volume-opt=o=bind,volume-opt=device=<PATH_TO_TRAINING_FOLDERS> -e PASSWORD=<PASSWORD> -p 8787:8787 ccdl/training_rnaseq:2019-philly

After starting your container this way, you can get to the RStudio window in a similar way as described above:

  • In Mac, type: localhost:8787 in your web browser.
  • In Windows, go to Command Prompt, type: ipconfig and click enter. Find the number that corresponds to the Virtual Box Host Network and the IPv4 Address. Copy and paste it. Put that number and :8787 at the end of it in your browser.

Resume with steps 6 - 9.