Using parPE with Snakemake¶
parPE comes with some rudimentary Snakemake workflow.
Parameter estimation¶
A very basic Snakefile for parameter estimation is located in snakemake/
.
This workflow is adapted to a specific model via a YAML configuration file.
An example is shown in
``snakemake/parpe_optimize_petab_steadystate.yaml` <../snakemake/parpe_optimize_petab_steadystate.yaml>`_.
An example¶
If parPE was built with examples, this workflow can be run after adapting
some paths in the example config file. petab.root
needs to be adapted to
reflect your parPE build directory, and probably you want to change the output
directories as well. The documented schema for this configuration file is
provided in snakemake/config.schema.yaml
.
After that you can run the full workflow with:
cd snakemake
snakemake --configfile parpe_optimize_petab_steadystate.yaml -- postprocess
This generates C++ code of the model, builds model specific binaries for
parameter estimation, runs parameter estimation, and processes the results.
After successful completion, you should see a file
results/figures/cost_trajectory.png
showing the optimizer trajectory.
The different snakemake targets are explained in the Snakefile and can be
accessed using snakemake --list
from the directory in which the Snakefile
is located.
To use this workflow with a different PEtab problem, you should only need to adapt the configuration file.