How to deploy a custom OBO dashboard¶
Contributed by @XinsongDu, edited by @matentzn
- Clone https://github.com/OBOFoundry/obo-nor.github.io and copy all its contents to a new GitHub repo under your account. Ensure that the
obo-nor.github.iorepo is also copied to your new repo (it is frequently skipped or hidden from the user in
Finderor when using the
cpcommand) and push to everything to GitHub.
- Pull the Ontology Development Kit from Docker Hub (can take a while):
docker pull obolibrary/odkfull
- Modify the
dashboard-config.ymlfile, in particular the
- Important: Add your ontology ID to the ID 'id' field
- Add the path to your ontology to the
- Get the "base uri namespace" of the ontology using the following steps: a. Open the ontology in Protégé b. Select a class and press "command + u" (MacOS), the stem of the path would be the base URI namespace (e.g., in EDAM ontology, the base uri namespace is http://edamontology.org/, for Uberon it would be http://purl.obolibrary.org/obo/UBERON_)
- Add the base uri namespace to 'base_ns' field of your ontology in the dashboard-config.yml
- (As of October 2021 make sure there are multiple ontologies in the dashboard-config.yml, otherwise errors would be reported while running the code. There are currently some bugs in the dashboard code that require at least 2 or 3 ontologies in the list).
- In the Makefile uncomment the
pip install networkx==2.6.2to ensure the correct network x version is installed.
sh run-dash.sh(make sure dashboard folder is empty before running, e.g.
rm -rf dashboard/*).
- When run successfully, push all changes to GitHub.
- Go to GitHub repo you just created, and go to Settings, then Pages, and select your main/master branch as "source", and your root directory. You will see a website URL highlighted in green, where your OBO dashboard is deployed.