FlyBase Release Database (Docker)

Run a local copy of the FlyBase Chado PostgreSQL database from the public release dumps.

This image is the same one used to host chado.flybase.org. Running it locally gives you faster queries, no shared rate limits, and the freedom to use any release version.

Quick start

git clone https://github.com/FlyBase/release-database-docker.git
cd release-database-docker
docker compose up -d

The first start downloads the release dump (~16 GB compressed) and loads it into PostgreSQL. This takes several hours. The database and the cached dump live in bind-mounted host directories (./data and ./dump-cache by default), so docker compose down will not delete them — data only goes away when you rm the host directories.

Disk usage peaks at ~180 GB during load (cached dump + database + WAL). Steady-state with the cached dump retained is ~172 GB; rm -rf dump-cache drops it to ~156 GB.

Once running, connect with:

psql -h localhost flybase flybase

(no password — trust auth on the flybase role)

Configuration

Env var	Default	What it does
RELEASE	current	Which release to load (e.g. FB2026_01, FB2025_05)
RELEASE_FILE	(auto-detected)	Override the dump filename if you know it
HOST_PORT	5432	Host port to bind PostgreSQL to
DATA_DIR	./data	Host path for the PostgreSQL data directory (bind mount)
DUMP_DIR	./dump-cache	Host path for the downloaded dump cache (bind mount)

Example: load a specific older release on a non-default port:

RELEASE=FB2025_05 HOST_PORT=5433 docker compose up -d

Refreshing for a new release

The data and dump cache are bind-mounted host directories, so you delete them yourself before the next load:

docker compose down
rm -rf data dump-cache
RELEASE=FB2026_02 docker compose up -d

Read-only access

The database is configured for strict read-only use. The flybase role:

• Has SELECT on all loaded Chado tables
• Cannot INSERT, UPDATE, DELETE, or TRUNCATE any table
• Cannot create temporary tables
• Cannot create new schemas
• Cannot create new databases

Connect as postgres (no password, localhost only) if you need to make local changes for your own analysis.

Tuning for smaller machines

The shipped config/postgresql.conf is tuned for a host with ~32 GB RAM. On a laptop with less memory you may want to lower:

• shared_buffers (currently 8GB → try 2GB)
• effective_cache_size (currently 24GB → try 4GB)
• work_mem (currently 100MB → try 32MB)
• maintenance_work_mem (currently 2GB → try 512MB)

Edit config/postgresql.conf and rebuild: docker compose up -d --build.

Notes

• The dump is loaded with autovacuum and fsync disabled because the data is static and reload-able from the public S3 location. This dramatically speeds the initial load.
• Connection limit is max_connections = 20. Raise it in config/postgresql.conf if you need more.
• Health status: docker inspect --format '{{.State.Health.Status}}' flybase-chado

Help

Open an issue on this repo, or email FlyBase via the contact form at https://flybase.org/contact/email.