Installation

First clone PathML’s repository:

git clone https://github.com/markowetzlab/pathml

PathML is best run inside an Anaconda environment. Once you have installed Anaconda, you can create pathml-env, a conda environment containing all of PathML’s dependencies, then activate that environment. Make sure to adjust the path to your local path to the PathML repository:

conda env create -f /path/to/pathml/pathml-environment.yml
conda activate pathml-env

Note that pathml-environment.yml installs Python version 3.7, PyTorch version 1.4, Torchvision version 0.5, and CUDA version 10.0. Stable versions above these should also work as long as the versions are cross-compatible. Be sure that the CUDA version matches the version installed on your GPU; if not, either update your GPU’s CUDA or change the cudatoolkit line of pathml-environment.yml to match your GPU’s version before creating pathml-env.

Some users have run into an error message saying that something from libvips is missing when PathML tries to import pyvips. This is because on some operating systems, the pip install of pyvips performed in the conda env create command leads to a flawed pyvips build. To solve this issue, also install pyvips using conda in pathml-env:

conda install -c conda-forge pyvips

For users who don’t wish to use conda, PathML can also be installed via pip. To do so, navigate to to the pathml directory containing setup.py, and run the following command:

pip install -e .