addgene/openbio/docs

Using the Docker container

Prerequisites

Docker runtime

To build and run Docker containers, you need to have Docker installed in your computer. If you are on a Mac or Windows, download and install Docker Desktop.

Building the Docker container

1. Download the addgene/openbio repository and move it to your Home folder. Unzip it by double-clicking on it. The top-level folder is called openbio-main
2. Launch the Terminal application and navigate to the top-level folder:

    cd openbio-main
   

3. Type the following command:

    docker compose build openbio
   

   This will take a few minutes.

Running the Docker container

To start the container, issue the following command:

 docker compose run openbio

This will take you to a shell prompt in the container. From this shell prompt you can use the Addgene Toolkit as explained here or in the individual command instructions.

Exit the container by typing the command exit at the shell prompt.

Working directory

Inside the container, the path/workdir should be used to specify input and output file paths. Please use this root path in parameters.yml.

The /workdir path is mapped by default to theopenbio-main/workdir folder in your host computer. This means that any files you place in the openbio-main/workdir folder will be available inside the container in the /workdir folder. Similarly, any files you create in the /workdir folder inside the container will be available in the openbio-main/workdir folder in your host computer. This is a convenient way to share your work files between the host computer and the container.

If you want to use a different folder in your host computer to share files with the container, start the container with the following command:

 OPENBIO_WORKDIR=[YOUR_DIRECTORY] docker compose run openbio

For example, if you want to use the host computer folder /Users/Harry/fastq-data, use the following command:

 OPENBIO_WORKDIR=/Users/Harry/fastq-data docker compose run openbio