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README.md

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Installation guide

Creating the environment

mamba create -n esa-hack -y

mamba activate -n esa-hack

Installing required packages

mamba install -c conda-forge ncbi-datasets-cli antismash pandas ipykernel -y
mamba install -c bioconda ncbi-genome-download -y

Setting up antiSMASH

# (ONLY FOR MAC) Fix nrpys installation (https://apple.stackexchange.com/a/443379)
pip uninstall nrpys
ARCHFLAGS="-arch arm64" pip install nrpys --compile --no-cache-dir
# Fix bcbio-gff installation (https://github.com/antismash/antismash/issues/713#issuecomment-2137807803)
mamba install bcbio-gff=0.7.0
# Download antiSMASH databases
download-antismash-databases

Additional dependencies

The parallel, rename and wget command line tools are required in order to run the scripts:

mamba install conda-forge::parallel bioconda::rename anaconda::wget -y