FISH Installation Guide

Follow the instructions to install anaconda on your machine (download the distribution that comes with python 3): https://www.anaconda.com/distribution/

After setting up anaconda, first downgrade/upgrade the setuptools to avoid confliction

sudo apt-get install openslide-tools

Next, clone our repo and use the environment configuration file located in docs/fish.yaml to create a conda environment:

git clone https://github.com/mahmoodlab/FISH.git
cd ./FISH
conda env create -n fish -f docs/fish.yaml

Activate the environment and install openslide-python:

conda activate fish
pip install openslide-python==1.1.1