= Install and first run
At https://github.com/CovertLab/WholeCellEcoliRelease/tree/7e4cc9e57de76752df0f4e32eca95fb653ea64e4[7e4cc9e57de76752df0f4e32eca95fb653ea64e4] you basically need to use the <Docker> image on <Ubuntu> 21.04 due to <pip (package manager)> 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:
``
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full
``
This mounts the host source under `/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
``
The meaning of each of the analysis commands is described at <output overview>{full}.
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.py` takes about 15 minutes, and it generates files such as `reconstruction/ecoli/dataclasses/process/two_component_system.py` (https://github.com/CovertLab/WholeCellEcoliRelease/issues/20[related]) which is required to run the simulation, it is basically a part of the build.
`runSim.py` does 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
``
and then it ended on the <ciro santilli s hardware/Lenovo ThinkPad P51 (2017)> at:
``
2569.18 783.09 1.943 1.910 2.005 1.950 1.963
Simulation finished:
- Length: 0:42:49
- Runtime: 0:09:13
``
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.