Installation

GIFTwrap is published on PyPI and can be installed using pip. It is compatible with Python 3.11 and later versions.

Warning

Ensure that you install giftwrap-sc, NOT giftwrap, which is an unrelated package.

Since the package provides a CLI, it is recommended to install it with pipx or uvx if you do not plan to use the python API, so that the CLI is available on your PATH and does not interfere with your current environment. In this case you can replace pip with pipx or uvx in the following commands.

Recommended installation:

pip install giftwrap-sc[all]

This installs the requirements for spatial data processing and basic summary analyses of paired WTA data.

Alternatively, you can install with fewer dependencies as follows:

pip install giftwrap-sc[analysis]  # For additional basic summary analysis
pip install giftwrap-sc[spatial]  # For spatial counts processing
pip install giftwrap-sc  # Minimal installation

Note

It is recommended that you have either cellranger or spaceranger installed in your system PATH if you plan to use the CLI as giftwrap will automatically detect cell barcode whitelists from these tools. If unavailable, it will try to revert to the cellranger default whitelist.