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 under
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:
The meaning of each of the analysis commands is described at Section "Output overview".
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:
and then it ended on the Lenovo ThinkPad P51 (2017) at:
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
when the cell had almost doubled, and presumably divided in 42 minutes of simulated time, which could make sense compared to the 20 under optimal conditions.
2569.18 783.09 1.943 1.910 2.005 1.950 1.963 Simulation finished: - Length: 0:42:49 - Runtime: 0:09:13