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jni / pia-tracking

Scripts to work with Pia Larsson's platelet tracking data
BSD 3-Clause "New" or "Revised" License
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Added install and uninstall scripts + environment file #13

Closed AbigailMcGovern closed 4 years ago

AbigailMcGovern commented 4 years ago

Changes As this repo has multiple dependencies, which would be painful to install one by one, I have written bash scripts for installation and for uninstalling the necessary python environment. I have checked that this works with recent scripts (i.e., has necessary dependencies for segmentation, viewing tracks, and tracking with btrack). Installation requires git and miniconda/anaconda.

Installation

cd path/to/pia-tracking
bash ./install.sh
conda activate platelet-tracking

Removal

conda deactivate 
bash ./uninstall.sh

NOTE: I wrote the uninstall.sh script because I had issues installing cv2 with pip and tried environments with various versions before installing with conda (which worked 🤷‍♀️). As a side note, I also had issues installing cv2 when I initially went to run the notebooks. It pretty much sucks!

ping @jni

jni commented 4 years ago

Boom! =)

AbigailMcGovern commented 4 years ago

Hehehe... apparently this was the most difficult bit