Installation

The development version can be installed with

# using pip
pip install git+https://github.com/pachterlab/seqspec@devel
# using uv
uv pip install git+https://github.com/pachterlab/seqspec@devel

The official release can be installed directly from pypi

# using pip
pip install seqspec
# using uv
uv pip install seqspec

Install from source if you want the current working tree.

# Python package with the Rust core
uv run maturin develop

# standalone Rust CLI
cargo install --path .

Verify the installation.

seqspec --version
seqspec auth path

seqspec accepts plain YAML and gzipped YAML (.yaml.gz). Remote resources can be configured with seqspec auth and used with --auth-profile in commands such as seqspec check and seqspec onlist.