Update to python >3

[EvavdL]

Would it be possible to update GLINT to be compatible with python 3?

[E-R]

Unfortunately, there are currently no plans to switch to python 3; the best solution for now os just working with two python environments in parallel.

[smoho]

It looks like a lot of these packages that are necessary for GLINT to function are not supported by python 2.7 anymore. I've followed all the instructions on the ReadME file but the issues I'm getting with are with version compatibility. Downloaded GLINT a year ago and it was working fine, but now it doesn't anymore and I need to update some results. Do you have any suggestions on how to move forward with this? Everything you've explained in the ReadMe has failed.

[E-R]

Can you please write the set of commands you used for setting up and installing the conda environment?

[smoho]

--create the conda environment

conda create -n python27 python=2.7 anaconda conda activate python27 conda install pip which python ~/.conda/envs/python27/bin/pip install numpy==1.16.6 ~/.conda/envs/python27/bin/pip install scipy==0.17 ~/.conda/envs/python27/bin/pip install scikit-learn==0.17.1 ~/.conda/envs/python27/bin/pip install pandas==0.19 ~/.conda/envs/python27/bin/pip install matplotlib==1.5.2 ~/.conda/envs/python27/bin/pip install statsmodels conda install -c conda-forge cvxopt conda install git git clone https://github.com/cozygene/glint.git ~/.conda/envs/python27/bin/python2.7 glint.py --datafile betas_part.txt --phenofile phenotype_part.txt --covarfile covariates_part.txt --gsave

[smoho]

Is there any update to this?

[E-R]

Not yet. It seems like the newer versions of pip and conda cannot reproduce the environment needed. This may require more time to resolve.