BioCracker

Parser for antiSMASH output GenBank files.

See the examples folder for usage examples.

Installation

Some BioCracker depdendencies rely on various command line tools to operate. These tools might not be available on all platforms. The pyproject.toml file specifies the core parser that is platform independent, but some functionality might be limited without the command line tools. BioCracker is designed to fail gracefully when some of these third party dependencies are not available.

We recommend installing BioCracker in a virtual conda environment, based on the provided environment.yml file to make sure all modules are available:

conda env create -f environment.yml

Installing PARAS

PARAS is used by BioCracker to predict substrate specificities of NRPS adenylation domains.

PARAS has no PyPI package ans must be installed from source manually:

pip install "paras @ git+https://github.com/bthedragonmaster/parasect.git@v2.0.0"

Installing HMMER2 on macOS Arm64

Use Rosetta to install the x86_64 version of HMMER2:

conda activate biocracker
conda config --env --set subdir osx-64
conda install hmmer2

Development

To set up a development environment, use the provided environment.dev.yml file:

conda env create -f environment.dev.yml