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Development

Running Changes Locally

You can mount files and folders into docker from your local system (VSCode Containers) to modify files within the image for testing and development.

local-docker-compose

You can also modify the local-docker-compose.yml file to mount folders into the Docker container by modifying the volumes section of the cdcs service.

In the cdcs step in the volumes section, you can add the paths of repositories to be changed. Here, we have an example mount for the meta-mdcs repository and core_main_app.

NOTE: Only meta-mdcs needs to be in /srv/curator/, other packages are mounted into the Python*.*/site-packages directory.

volumes:
    ......
    - META-MDCS_PATH:/srv/curator/
    - CORE_MAIN_APP_PATH/core_main_app:/usr/local/lib/python3.8/site-packages/core_main_app

Example:

Here is a working example of the lines added to the volumes section of the cdcs service in local-docker-compose.yml.

volumes:
    ......
  - ~/Documents/github/Meta-Genome-Org/meta-mdcs:/srv/curator/
  - ~/Documents/github/Meta-Genome-Org/core_main_app/core_main_app:/usr/local/lib/python3.8/site-packages/core_main_app

With these changes in the local-docker-compose.yml, you can then start the software with the command:

docker-compose up

See: Tips for customizing CDCS (NexusLIMS) for more guidance on making changes to the system.