Phylesystem is a series of git repository used to store phylogenetic statements (typically published trees). You can download the full set of phylesystem shards (there is only one, at this point) by following the instructions on and then pointing peyotl to your local copy of phylesystem as described on the Configuration page.

If you have a local copy of the phylesystem, then you can peyotl’s PhylesystemAPIWrapper to use your local copy by using get_from='local' when creating an instance of the wrapper:

from peyotl.api.phylesystem_api import PhylesystemAPI
phylesystem_api_wrapper = PhylesystemAPI(get_from='local')
local_phylesystem_controller = phylesystem_api_wrapper.phylesystem_obj
for study_id, file_path in local_phylesystem_controller.iter_study_filepaths():
    print study_id, 'is in', file_path

You can perform the phylesystem_api functions on a local version of the PhylesystemAPI class, as well. But the wrappers created using get_from='local' are the only ones that allow you to iterate over all studies.

The scripts/phylesystem/ script demonstrates iterating over every study in a local version of the repository and printing the study and tree tags.

Note that phylesystem section of the configuration file has settings that control the size of files allowed in the phylesystem.