pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
GNU General Public License v3.0
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Graphical User Interface Beta Testers #11

Open pblischak opened 5 years ago

pblischak commented 5 years ago

I've been working on a v1.0 release of HyDe that cleans up and reorganizes the code and moves support over to Python 3.6+ only. The visualization module is being removed as well.

I've also spend a good amount of time trying to develop a GUI for HyDe. However, I've been running into issues on macOS Mojave because of problems with the tk/tcl and tkinter packages not communicating properly. After searching around, this is a known bug but I still can't seem to get the GUI to work on my Mac. It works fine on Ubuntu 18.04 LTS though.

If there are any users that wouldn't mind helping me out by testing to see if they can get the GUI working on their machines, it would be a huge help. Thanks in advance!

# This assumes you are using miniconda3
conda create -n hyde-env python=3
conda activate hyde-env

# Install HyDe's dependencies
pip install cython numpy multiprocess

# Now clone HyDe and checkout the v1.0.0 branch
git clone https://github.com/pblischak/HyDe.git
cd HyDe/
git checkout v1.0.0

# Install v1.0.0 of HyDe
python setup.py install

# Go into the scripts folder and run
# the GUI
cd scripts/
python hyde_gui.py
pblischak commented 5 years ago

To run an actual analysis in the GUI, you can navigate to the folder with your input data files using a terminal window, and then instead of using one of the *_hyde.py scripts to do an analysis from the command line, just type hyde_gui.py. If it works, a window should pop up that lets you type in all of the info for your analysis. Hitting the Run button or pressing <Enter> should start the analysis. Any errors and/or run info will be printed in the terminal.

I forgot to mention, you also need to install the progress package for printing a progress bar while the analyses run:

pip install progress