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 .