Environment Settings

Configuration Location

Magellon is configured through a .env file in the Docker/ directory. Start from the example and edit in place:

cp .env.example .env

Core paths

MAGELLON_HOME_PATH=/magellon/home
MAGELLON_GPFS_PATH=/magellon/gpfs
MAGELLON_JOBS_PATH=/magellon/jobs

These map into each container at fixed mount points, so code inside the stack can assume /gpfs, /jobs, and the home directory without any per-deploy changes.

Common overrides

Default Configuration

.env.example ships with sensible defaults for a single-node Docker install. Most deployments run unmodified — only touch these settings when your environment differs from the bundled stack.

Area	Default	When to override
Database credentials	Bundled MySQL container	Pointing at an external database
Logging level	Quiet defaults per service	Raise to DEBUG to diagnose failures; lower to WARN in production
GPU selection	All visible GPUs	Set CUDA_VISIBLE_DEVICES to pin specific cards for motion correction

GPU Pinning Example

To restrict the motion-correction plugin to specific GPUs:

CUDA_VISIBLE_DEVICES=0,1