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frankligy / NeoAntigenWorkflow

NeoAntigenWorkflow
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For developer: in cluster how to build the environment? #2

Open frankligy opened 4 years ago

frankligy commented 4 years ago

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 commented 3 years ago

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