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manuel-munoz-aguirre / PyHIST

A pipeline to segment tissue from the background in histological images
GNU General Public License v3.0
64 stars 13 forks source link

Portability #5

Closed manuel-munoz-aguirre closed 5 years ago

manuel-munoz-aguirre commented 5 years ago

The fact that the pipeline is written in bash, forces the user to run it on a Linux environment (i.e. this leaves out Windows users). Since it is mostly calling other scripts, creating files/folders, we can consider two options:

  1. Leave the pipeline written in bash. Prepare a docker container to encapsulate everything (it would not be a python package in this case)
  2. Write the pipeline in pure Python. Deploy the pipeline just as a Python package that can be ran in any system just by installing with pip, as long as the necessary dependencies are met
manuel-munoz-aguirre commented 5 years ago

Decided to dockerize and run with python script, no python package