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.
Choose from: "alphafold", "gpt", "cellxgene", "elm", or "cbio"

Optional arguments
-o --out
Only applies when module='elm'. Path to a folder where the raw ELM database files (elm_instances.fasta, elms_classes.tsv, elm_instances.tsv, elm_interaction_domains.tsv) will be downloaded — useful if you want a local copy of the ELM data for your own scripts or inspection, separately from running gget elm.
NOTE: To set up the files so that gget elm can use them, omit this argument — gget elm only reads from the default location inside the gget package installation folder. Files downloaded to a custom --out path will not be picked up by gget elm.
Default: None (downloaded files are saved inside the gget package installation folder where gget elm can find them).

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.