Getting started

Retropaths was designed to work in Jupyter Lab.

Installing Retropaths

If this is your first time opening jupyter lab you need to create a conda environment. Navigate to the retropaths repository and execute the following command. You must have Anaconda3 installed, preferably python version>=3.8 conda env create --name rp --file=environment.yml. This will download and install all of the python dependencies which are necessary to run retropaths.

Running

You need the oe_license.txt in your data directory. This is a proprietary license distributed by OpenEye. There are several environment variables that need to be activated. These are in the file exports.sh bash export PYTHONPATH="$PYTHONPATH:$(pwd)" export SHELL=/bin/bash export retro_folder=$(pwd) export OE_LICENSE=$(pwd)/data/oe_license.txt export TEMPLATE_FOLDER=$(pwd)/data/ export OMP_NUM_THREADS=1 The launch.sh bash script loads the environment variables and starts Jupyter Lab.

To run Jupyter Lab first make sure the conda environment is activated conda activate rp. Then execute ./launch.sh

A Jupyter lab window should appear. If it doesn't, copy the URL that appears in the terminal and paste it into a browswer. You can open a python file as a Jupyter Notebook by navigating to the file using the finder pane on the left hand side, and then right clicking on a python file and opening as Jupyter Notebook. (This only works because we have a package installed, normally you cannot open python files as notebooks)