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Environment

The genomics environment is created by scripts/env/install.sh (see Installation). Use the project activation script instead of calling conda activate genomics manually:

source scripts/env/start_genomics_universal.sh

The universal script:

  • detects common Conda/Miniforge locations;
  • activates the genomics environment;
  • cleans problematic CUDA library paths on affected systems;
  • loads Bash completion for genomics when the command is installed.

If your Conda installation is always under ~/miniforge3, this simpler script is also available:

source scripts/env/start_genomics.sh

Completion

The activation scripts run this automatically:

source <(genomics completion bash)

To install completion persistently for your user:

mkdir -p ~/.local/share/bash-completion/completions
genomics completion bash > ~/.local/share/bash-completion/completions/genomics

AlphaGenome server environment

The local AlphaGenome model server does not run in genomics: it needs JAX with CUDA, TensorFlow and alphagenome>=0.7, which conflict with PyTorch. genomics alphagenome server setup creates a second conda environment, alphagenome (or a venv inside the alphagenome_research checkout when there is no conda), and the visualizer and genomics alphagenome server start run the server with its interpreter. You never need to activate it. Override the choice with ALPHAGENOME_SERVER_PYTHON / ALPHAGENOME_SERVER_DIR.

Variable Default Meaning
ALPHAGENOME_API_KEY – (also read from ~/.env) hosted API key
ALPHAGENOME_ADDRESS – use a self-hosted server, e.g. grpc://127.0.0.1:50051
ALPHAGENOME_TLS_CA_CERT – CA certificate of a self-signed TLS server
ALPHAGENOME_SERVER_DIR ../alphagenome_research, then ~/.local/share/genomics/alphagenome_research checkout used for the local server
ALPHAGENOME_SERVER_PYTHON the env alphagenome or another env with CUDA jax interpreter of the local server
ALPHAGENOME_SERVER_HOST / ALPHAGENOME_SERVER_PORT 127.0.0.1 / 50051 where the local server listens
GENOMICS_DATA_ROOT / GENOMICS_RESULTS_ROOT /dados/GENOMICS_DATA / results/ datasets / runs and caches