segNET

This github webpage is reserved for the future versions of segNET. The full documentation will be available at the following link. Stay tuned!

• Free software: GPLv3 license
• Full documentation: https://segnet.readthedocs.io/en/latest/readme.html

Installation

Note: Although segNET will be available at PyPI for pip install or easy_install, we still recommend using Anaconda distribution of python to install all the dependencies without issues. We are going to post segNET on Anaconda Cloud soon, so add the following channels if you have not already:

$ conda config --add channels r
$ conda config --add channels bioconda

To avoid conflicts among dependencies, we also highly recommend using conda virtual environment and install segNET in it:

$ git clone https://github.com/kbchoi-jax/segnet
$ cd segnet
$ conda create -n segnet python=2
$ source activate segnet
(segnet) $ conda install scipy
(segnet) $ conda install networkx
(segnet) $ conda install matplotlib
(segnet) $ conda install Click
(segnet) $ python setup.py install

That's all! Now segNET is ready. Once you are done using segNET, you can go out from its virtual environment anytime:

(segnet) $ source deactivate

Usage