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Using a machine with miniconda the followin set of commands seem to work:
cd diffacto/src/ conda create -n diffacto_pack_35 python=3.5 source activate diffacto_pack_35 conda install numpy scipy pandas networkx scikit-learn pip pip install pyteomics pyinstaller pyinstaller --hidden-import pandas._libs.tslibs.timedeltas --hidden-import scipy._lib.messagestream --onefile run_diffacto.py