Docker Container Set Up - from Flashdrive

October 7, 2019 ยท View on GitHub

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.

Part 1: Get the Docker image using a copy from the flash drives

  1. Be sure that you have copied ccdl_training_rnaseq.tar.gz from the flash drive as was instructed in these steps. If you do not have this file yet, follow those instructions before attempting to complete these next steps.

Next steps

Next steps for Mac OS X and Linux users

  1. Open Terminal. You can use Spotlight Search on a Mac to find this application.

  2. You can navigate to your Desktop directory by copying and pasting this command into Terminal (hit Enter):

cd Desktop
  1. Once you are in your Desktop directory, you must extract the file with the following command:
gunzip ccdl_training_rnaseq.tar.gz
  1. You can then load the Docker image with docker load:
docker load -i ccdl_training_rnaseq.tar

This will take a minute.

  1. When this step completes, check that it was successful with:
docker images

You should see output like:

REPOSITORY                         TAG                 IMAGE ID            CREATED             SIZE
ccdl/training_rnaseq               2019-philly            16eb55269eec        19 minutes ago      5.03GB

Note that the created field may not match.

Next steps for Windows 10 Pro users

  1. Install 7-Zip install if you do not already have it by downloading the 64-bit x64 program here: https://www.7-zip.org/

  2. Right-click ccdl_training_rnaseq.tar.gz.

  3. Go to 7-Zip and selected Extract Here. When that has finished extraction, you should see ccdl_training_rnaseq.tar on your Desktop.

  4. Open your Command Prompt application.

  5. Navigate to your Desktop directory with:

cd Desktop
  1. You can load the Docker image with docker load:
docker load -i ccdl_training_rnaseq.tar

This will take a minute.

  1. When this step completes, check that it was successful with:
docker images

You should see output like:

REPOSITORY                         TAG                 IMAGE ID            CREATED             SIZE
ccdl/training_rnaseq               2019-philly            16eb55269eec        19 minutes ago      5.03GB

Note that the created field may not match.

Part 2: Run the Docker container (all operating systems)

  1. Run the container. Change the <PASSWORD> in the line below to whatever you'd like. Make sure to get rid of < and >. Also note that your chosen PASSWORD cannot have a $.
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. If you do not see the training modules folders in the kitematic folder, raise your hand.

  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 step 5 of part 2.