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qin-yu/install-cvapipe-analysis.md

Created March 29, 2025 00:53
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install-cvapipe-analysis.md

Installation instruction for the cvapipe_analysis software

  • cd to the folder where you put folders of your softwares
  • download the repository by git clone https://github.com/AllenCell/cvapipe_analysis.git
  • go into the downloaded repo cd cvapipe_analysis
  • use the publication version of the code git checkout tags/nature-paper
  • create a new Conda environment conda create --name cvapipe python=3.8 and activate it conda activate cvapipe
    • If you don't know conda please check out my documentation: Install Mamba
  • install the downloaded code pip install -e .
  • test if it runs: Running the pipeline to reproduce the paper
    • Make sure you start with cvapipe_analysis loaddata run --test (not the first one which would download 7Tb data for you).
  • Installation is done.
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