Guide for setting up pipeline (not complete, please help!)

(0) Read some other parts of this wiki so you understand how the pipeline is supposed to work (pipeline overview).

(1) Install Ubuntu 16.04.3 LTS. This is important if you want to use MountainSort. The post-sorting part of the code only needs Python (and potentially R).

(2) Install conda (we have 4.5.4)

check if this worked on the terminal by checking the version of conda you installed:

conda -V

(3) Make a conda environment. We use PyCharm and make the environment in Settings/ProjectInterpreter

(4) Install the following Python packages: pandas, joblib, cmocean, scipy, matplotlib, numba, xlrd, rpy2, skimage (scikit-image)

(the rest of the dependencies seem to be included in conda)

(5) Install MountainSort 3 (Version: 0.11.5) and test if it works following the instructions in the MS docs

(6) Change the folder paths in control_sorting_anlysis.py to your own

Good luck, and please give us feedback (in issues) on these instructions so they eventually become more helpful. Thank you!