Python arguments are equivalent to long-option arguments (--arg), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the -h --help flag.

gget setup 🔧

Function to install/download third-party dependencies for a specified gget module.

Note: Some dependencies (e.g., cellxgene-census) may not support the latest Python versions. If you encounter installation errors try using an environment with an earlier Python version.

Positional argument
module
gget module for which dependencies should be installed.

Optional arguments
-o --out
Path to the folder downloaded files will be saved in (currently only applies to module = 'elm').
NOTE: Do NOT use this argument when downloading the files for use with gget.elm.
Default: None (downloaded files are saved inside the gget package installation folder).

Flags
-q --quiet
Command-line only. Prevents progress information from being displayed.
Python: Use verbose=False to prevent progress information from being displayed.

Example

gget setup alphafold

# Python
gget.setup("alphafold")

→ Installs all (modified) third-party dependencies and downloads model parameters (~4GB) required to run gget alphafold.