At 7e4cc9e57de76752df0f4e32eca95fb653ea64e4 you basically need to use the Docker image on Ubuntu 21.04 due to pip breaking changes... (not their fault). Perhaps pyenv would solve things, but who has the patience for that?!?!
The Docker setup from README does just work. The image download is a bit tedius, as it requires you to create a GitHub API key as described in the README, but there must be reasons for that.
Once the image is downloaded, you really want to run is from the root of the source tree:This mounts the host source underThe meaning of each of the analysis commands is described at Section "Output overview".
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full
/wcEcoli, so you can easily edit and view output images from your host. Once inside Docker we can compile, run the simulation, and analyze results with:
make clean compile && python runscripts/manual/runFitter.py && python runscripts/manual/runSim.py && python runscripts/manual/analysisVariant.py && python runscripts/manual/analysisCohort.py && python runscripts/manual/analysisMultigen.py && python runscripts/manual/analysisSingle.py
As a Docker refresher, after you stop the container, e.g. by restarting your computer or running
sudo docker stop wcm, you can get back into it with:
sudo docker start wcm sudo docker run -it wcm bash
runscripts/manual/runFitter.pytakes about 15 minutes, and it generates files such as
reconstruction/ecoli/dataclasses/process/two_component_system.py(related) which is required to run the simulation, it is basically a part of the build.
runSim.pydoes the main simulation, progress output contains lines of type:
Time (s) Dry mass Dry mass Protein RNA Small mol Expected (fg) fold change fold change fold change fold change fold change ======== ======== =========== =========== =========== =========== =========== 0.00 403.09 1.000 1.000 1.000 1.000 1.000 0.20 403.18 1.000 1.000 1.000 1.000 1.000
2569.18 783.09 1.943 1.910 2.005 1.950 1.963 Simulation finished: - Length: 0:42:49 - Runtime: 0:09:13