Installation

Requirements

abstar requires Python 3.9 or later.

MMseqs2 is used internally for germline gene assignment, but it is bundled with abutils (a dependency of abstar), so no separate installation is required.

Install abstar

The easiest way to install abstar is via pip:

pip install abstar

Using a Custom MMseqs2 Binary

If you prefer to use a specific version of MMseqs2 rather than the bundled binary, you can specify the path to your custom binary using the mmseqs_binary parameter:

import abstar

sequences = abstar.run("sequences.fasta", mmseqs_binary="/path/to/mmseqs")

See the MMseqs2 installation guide for information on installing MMseqs2.

Docker

abstar is included in the brineylab datascience Docker container:

docker pull brineylab/datascience
docker run -it brineylab/datascience

This container includes abstar and all dependencies pre-configured.

Development Installation

To install from source for development:

git clone https://github.com/briney/abstar
cd abstar/
pip install -e .

Verify Installation

To verify that abstar is installed correctly:

python -c "import abstar; print(abstar.__version__)"