Getting Started

Build the CLI:

cargo build --release

Install this checkout so genesets-rs can be run from any directory:

cargo install --path /path/to/genesets-rs --force

Cargo writes the binary to ~/.cargo/bin/genesets-rs. If your shell cannot find it, add Cargo’s bin directory to your PATH:

echo 'export PATH="$HOME/.cargo/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

Run the bundled ontology-style example:

genesets-rs enrich \
  --annotations examples/gene_terms.tsv \
  --terms examples/terms.tsv \
  --closure examples/closure.tsv \
  --sample examples/sample.txt \
  --background examples/background.txt \
  --overlap-genes

Run all ontology terms against all ontology terms:

genesets-rs matrix \
  --annotations examples/gene_terms.tsv \
  --terms examples/terms.tsv \
  --closure examples/closure.tsv \
  --queries-from-targets \
  --background examples/background.txt

Run from YAML:

genesets-rs run examples/enrich.yaml

Relative paths inside a YAML config are resolved from the config file’s directory, so this also works from outside the repository:

genesets-rs run /path/to/genesets-rs/examples/enrich.yaml

For development without installing, use cargo run -- before the same CLI arguments:

cargo run -- run examples/enrich.yaml

Install or run the optional workflow layer when you want repeatable source prep, GO/Reactome evals, Parquet summaries, and report metadata:

uv run --project python/genesets-workflows genesets-workflows doctor

The workflow layer calls the Rust CLI for batch compute; it is not required for simple one-off enrichment.

Build the documentation site locally:

cargo install mdbook
mdbook serve

Run the test suite:

cargo test

Run the benchmark harness:

cargo bench