Guidelines for adding VICE tools in DE¶
Adding VICE tools in DE is different from regular DE tools. Currently the process is not automated and so for now, you’ll have to follow certain guidelines which are listed below. Before you add your VICE tools..
- Figure out if you’re going to need additional configuration for the tool
Some tools will require additional configuration in order to get them working correctly with the VICE feature. So please make sure
- To ensure that the listen port for the web UI has a sane default and is set.
- To ensure that the working directory is sane and working.
- To ensure that the commonly needed dependencies are installed in the container image.
- To ensure that the default user is already available.
- To disable authentication (CyVerse provides CAS authentication and authorization).
- URLs will work sanely behind a reverse proxy. If they don’t, you may need to add nginx to the container.
- Use community images as a base image
If you need to set the configurations at all (see above), you’ll need to create a new Dockerfile that uses the community-provided image as a base. Your new Dockerfile should deal with custom configurations and dependency installations.
- Jupyter-Lab (https://hub.docker.com/r/discoenv/jupyter-lab)
- Rstudio (https://hub.docker.com/r/discoenv/rstudio-nginx)
- Shiny (https://hub.docker.com/r/discoenv/shiny)
See some examples of VICE apps that uses community images as base image in the Dockerfile
- MMTF (https://github.com/sbl-sdsc/mmtf-genomics/blob/master/vice/Dockerfile)
- Rstudio-Bioconductor (https://github.com/cyverse/docker-builds/blob/master/rstudio-bioconductor/Dockerfile)
- Patmatch (https://github.com/fomightez/patmatch-binder/tree/master/vice)
- Test your Docker image
Since the images are built based using Dockerfile, make sure you test the Dockerfile before providing it to us. Dockerfile must have Entrypoint. If you cannot provide us the Dockerfile, you can request integration of the app by doing a tool request.
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