Installation

We recommended installing the library within a separate conda environment running Python 3.10 or 3.11. Python 3.12 is currently not supported.

conda create -n "scPortrait" python=3.11
conda activate scPortrait

Optional: Installing the stitching capabilities of scPortrait

The stitching capabilities of scPortrait require a working Java installation. If not already installed, you can download the latest version of Java from the official website or install it via mamba or conda:

Important

Java needs to be installed before installing scPortrait. Otherwise when trying to access the stitching capabilities of scPortrait, an error will be raised that Java is not found at the indicated path.

conda install -c conda-forge openjdk

If you wish to utilize the accelerated stitching backend you need to install the graph-tool library. This library is not available via pip and needs to be installed separately via conda.

conda install -c conda-forge graph-tool==2.68

To install the latest release of scPortrait:

pip install git+https://github.com/MannLabs/scPortrait