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Installation Guide

To install the most basic version of this project, create a python virtual environment and run:

pip install git+https://github.com/ImperialCollegeLondon/ReCoDe-spatial-transcriptomics.git

However, there are some analysis modules that use the tool MuSpAn, which requires a license to install. If you want to use those modules, you will need to request a license. Do this by following the link in the MuSpAn installation instructions. Once you have your username and password, run the following command and enter them when prompted.

pip install 'recode_st[muspan] @ git+https://github.com/ImperialCollegeLondon/ReCoDe-spatial-transcriptomics.git'

Development installation

To install the development version of the software, clone this repo and run

pip install -e ".[dev,muspan]"

Pinned versions of the dependencies are saved in two text files:

  • requirements-muspan.txt
  • requirements-muspan.txt

These are managed by pip-tools, which is a dependency. They are built using the pip-compile command at the top of each file. You can also clean your current environment by ensuring it is in-sync with the following commands:

pip-sync requirements*.txt
pip install -e .

A note for Intel Macs

The newest versions for some packages do not support older Macs with Intel CPUs.

One known issue is the pip install above works but you are seeing failures when running the code. Specifically this message followed by a segmentation fault:

OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

In this case, you should use conda to install the packages. There is an environment.yml file provided that will create a conda environment called recode_st. To fully install it, do the following:

cd ReCoDe-spatial-transcriptomics # Ensure you are in the root directory of the repo
conda env create -f environment.yml
conda activate recode_st
pip install --no-build-isolation --no-deps -e .
pip install https://docs.muspan.co.uk/code/latest.zip # If you need the MuSpAn modules