For developer: in cluster how to build the environment?

[frankligy]

Here's the guideline:

conda create -p mhcEnv python=3.6
pip install mhcflurry
pip install Biopython matplotlib requests pathos xmltodict
pip install torch torchvision
mhcflurry-downloads fetch models_class1_presentation
# when doing above, properly upgrade or downgrade relevant package if conflicting occur

[frankligy]

Update on Sep 6th

In order to run NeoEpitope.py (receptor finding algorithm)

pip install regex

And configure TMHMM and corresponding dependencies as stated in TMHMM function in NeoEpitope.py and sub_py.sh

# these two lines should be run before running NeoEpitope.py
module load perl/5.20.1
export PATH=$PATH:/data/salomonis2/LabFiles/Frank-Li/python3/TMHMM/tmhmm-2.0c/bin