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ome / EMBL-EBI-imaging-course-05-2023

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Cellprofiler environment #16

Open dominikl opened 10 months ago

dominikl commented 10 months ago

The current environment_cp.yml didn't work for me. First problem was that omero-py and wxpython couldn't be installed, some version conflicts. So I created an empty env and installed omero-py and wxpython first manually, then removed them from the yml and installed the remaining stuff from the env yml. Second problem was that cellprofiler 4.2.4 didn't compile. Changed the line to git+https://github.com/CellProfiler/CellProfiler.git@v4.2.6 to install 4.2.6. This worked, but the notebook then failed with import error related to pillow. Uninstalled OS libtiff with brew uninstall libtiff (I don't know if that was really necessary), then reinstalled pillow. Then it worked.

dominikl commented 10 months ago

Btw, I tried to export this enviroment with conda env export --no-builds >> environment_cp.yml but the resulting yml can't be restored again (just lots and lots of conflict errors).

pwalczysko commented 10 months ago

cc @jburel - note that on Mac M1 the cp install works as written in Day_4 - but not on my old Mac, where the package "Centrosome" from CP fails to install.

dominikl commented 10 months ago

With 4.2.4 I got a cython compile error in some kind of "Centrosome" file too.