What you need

You need to have a laptop/desktop with the following software installed (see detailed instructions below)

  • Docker
    • Having a docker user account is not necessary for the purposes of the tutorial.
  • IGV

Download docker image

Please download the docker image we have prepared for the purposes of this tutorial before the tutorial. The size of docker image is approximately 20GB.

You can use the following command:

docker run -it -P --name epigenomics -v ~/container-data:/data sivarajank/epigenomics_tutorial:latest

Command for Windows users:

docker run -it -P --name epigenomics -v C:\Users\*username*\Documents\container-data:/data sivarajank/epigenomics_tutorial:latest

Please do not forget to change your username.

The name parameter assigns a name to your docker image. If you used the above command it is epigenomics (–name). If, for some reason, you exit or abort your docker image, you can use the following commands to re-login to the docker container. :

docker start epigenomics
docker attach epigenomics

To get out of the docker container, you can simply type exit.

If, for some reason, we ask you to update the docker container, you need to exit the docker container and execute:

docker pull sivarajank/epigenomics_tutorial:latest

After that you can execute the docker start and attach commands mentioned earlier.

How to access data inside the docker container

We recommend to access the data inside the container using the proposed method, for the purposes of this tutorial.

In the aforementioned docker run command you might have noticed the -v ~/container-data:/data parameter. This parameter enables you to access any data you have inside the /data directory of your container from your local machine at ~/container-data/. The /data directory is mirrored to your local ~/container-data/ folder, meaning that everything you do (remove, edit, add etc.) in you local folder ~/container-data/ will also be changed in the /data folder and vice-versa. This has the advantage that we can create files like plots inside of Docker, write them to the /data directory and you can easily access them outside of Docker by looking into the ~/container-data/ folder.

We have shipped some preprocessed data as part of our container which can be found at /root/EpigenomeAnalysisTutorial-2020. Once you are inside the docker container, please run the following command so that you can access this data from your local machine to view in IGV or view the plots :

mv /root/EpigenomeAnalysisTutorial-2020 /data/
cd /data

Now, you can find the folder EpigenomeAnalysisTutorial-2020 in your local machine at ~/container-data/ folder. We will run all commands under this folder during the course of the tutorial. Please take care to keep this directory as you current directory.

cd EpigenomeAnalysisTutorial-2020

How to remove all the containers and images after the tutorial

If you want to remove all docker content (images/containers) from your system, you can run the following commands:

docker rm epigenomics
docker image prune -a