Install these dependencies according to their own instructions:
- NodeJS version 16+
- Postgres
- Used for storing SNPs, features, associations (p-values), and other metadata.
- Tested with versions 13 through 15.
- See Setting up the Postgres database for how to prepare this.
- Redis
- Used for caching values
- Tested with version 6+
- note that a Redis instance should never be exposed to the internet!
EpiVar expects it to be available locally at
localhost:6379; the default Redis port.
bw-merge-window: https://github.com/c3g/bw-merge-windowbigWigSummary: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
TODO: Docker compose setup
This is a standard Express backend + React frontend application. Frontend files
live in ./client, and backend files live at the root of the project.
The API routes are set up in app.mjs, and are listed in routes/;
the frontend groups all API communication functions in ./client/src/api.js.
The models/ folder contains the functions to retrieve the actual data,
depending on where it is. Some of it is in Postgres databases (genes, peaks, sessions); the tracks
come from the tracks / mergedTracks folders configured previously, the variants (aka samples)
data comes from a VCF, and the UCSC track hubs are generated on the fly.
Note that all code should be written with the assumption that multiple processes can run at a time. Thus, Redis/Postgres should generally be used for any cached/persistent data.