We offer Docker images of the crisprVerse ecosystem on the Docker Hub. The image contains the following conponents:

• R installation (currently 4.2.1)
• crisprVerse R packages and their dependencies
• ViennaRNA 2.5.1
• RNAhybrid 2.1.2

Convienently, all Python conda environments needed for crisprScore are also already installed in the Docker image.

Obtaining the Docker image

The Docker image can be pulled directly from the Docker Hub using the following command

docker push fortin946/crisprverse:dev

Note that this requires Docker to be installed on your machine. See the Docker website for instructions.

Usage

Once the image is pulled, users can start an R session from the container using the following command:

docker run -it fortin946/crisprverse:dev

Alternatively, one can access the container within the terminal without starting an R session by typing the following command:

docker run -it fortin946/crisprverse:dev /bin/bash

Finally, to be able to access and write files to the local file system, users can mount a specific folder using the usual -v option. For instance, suppose we want to mount a local folder /Users/fortinj2/crisprIndices to a folder called /home/crisprverse/indices inside of the container, we can use the following command to do so:

docker run -it -v '/Users/fortinj2/crisprIndices:/home/crisprverse/indices' fortin946/crisprverse:dev

To illustrate this, the following lines

docker run -it -v '/Users/fortinj2/crisprIndices:/home/crisprverse/indices' fortin946/crisprverse:dev  /bin/bash
ls indices

will list the files available in the /Users/fortinj2/crisprIndices folder as it it mounted to the indices folder inside of the container. For more information about volume and mounting, see the Docker documentation.

Modifying the Docker image

Users can use our Dockerfile as a starting point to modify or customize the Docker image.