Installation

PyPI

All third-party dependencies are installed automatically via pip, simply run:

python -m pip install deltapd

Docker

The container must be able to access the input data, and write output data. Therefore, you must specify a volume mapping (-v host:container), e.g. the host path /tmp/deltapd is mapped to the container path /data

Note: --plot will not work as it requires a display for PyQt.

docker run -v /tmp/deltapd:/data deltapd:latest --r_tree /data/ar122_reference.tree --q_tree /data/ar122_ssu_query.tree --metadata /data/ar122_metadata_r95.tsv --msa_file /data/ar122_ssu_r95.fna --influence_thresh 2 --diff_thresh 0.10 --out_dir /data/deltapd_out --k 20 --cpus 10