This project demostrates running FlepiMoP using Cromwell, Python, R, and Docker.
- JAVA must be installed and be a minimum version of 11.
- Docker must also be installed.
Please note: The cromwell workflow script will check for these requirements and stop execution if they are not met.
- Create your model configuration file according to FlepiMoP specifications and save it in this folder.
- Please specify in your model for input files to be in the model_inputs folder.
- Place all of your input files in the model_inputs folder.
- Edit model_specs.json using a text editor to specify the model configuration file as well as the executable, then save.
{
"flepiMoPWorkflow.model_configuration_yml": "config_sample_2pop.yml",
"flepiMoPWorkflow.model_executable": "gempyor-simulate"
}
{
"flepiMoPWorkflow.model_configuration_yml": "config_sample_2pop_inference.yml",
"flepiMoPWorkflow.model_executable": "Rscript flepiMoP/flepimop/main_scripts/inference_main.R"
}
- From the command line execute the Cromwell workflow.
./cromwell_workflow.sh
If the workflow Succeededb>, results will be inside the model_output folder.
If the workflow Failed, see stderr file in the model_output folder.
For additional information, see stdout file in the model_output folder.