Currently, the annotations building step requires PDB_Tool added to the user $PATH, so for now we could add a PDB_Tool installation step on the docs during the installation of Oncodrive3D, or we could provide a container to make it run with singularity as shown in the commented code.
https://github.com/bbglab/clustering_3d/blob/ff9875ad0a6bd0017ff2c5edf37942dbf187b153/scripts/plotting/pdb_tool.py#L39-L59
Linked to #12
