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 the json where the input files for your model are located. The default setting is 'model_input'.
- Place all of your input files in this folder.
- Edit modelWorkflow_inputs.json using a text editor to specify the model configuration file as well as the executable, then save.
{
"modelWorkflow.run_Model.name_of_this_model_run": "flepimop",
"modelWorkflow.run_Model.model_configuration_yml": "config_sample_2pop.yml",
"modelWorkflow.run_Model.model_executable": "gempyor-simulate",
"modelWorkflow.run_Model.model_input_folder": "model_input",
"modelWorkflow.run_Model.model_git_repository": "https://github.com/HopkinsIDD/flepiMoP.git",
"modelWorkflow.run_Model.model_output_folder": "model_output",
"modelWorkflow.run_Model.model_output_file_types": "[parquet]",
"modelWorkflow.run_Model.install_model_script": "./scripts/sh/flepimop/install_model.sh",
"modelWorkflow.run_Model.run_model_script": "./scripts/sh/flepimop/run_model.sh",
"modelWorkflow.run_Model.model_runtime_docker": "rocker/verse:latest",
"modelWorkflow.setup_os_script": "./scripts/sh/setup_os.sh",
"modelWorkflow.clone_repository_script": "./scripts/sh/clone_git_repository.sh",
"modelWorkflow.copy_cromwell_logs_script": "./scripts/sh/copy_cromwell_logs.sh",
"modelWorkflow.copy_model_output_script": "scripts/python/copy_model_output.py"
}
{
"modelWorkflow.run_Model.name_of_this_model_run": "flepimop",
"modelWorkflow.run_Model.model_configuration_yml": "config_sample_2pop_inference.yml",
"modelWorkflow.run_Model.model_executable": "Rscript flepiMoP/flepimop/main_scripts/inference_main.R",
"modelWorkflow.run_Model.model_input_folder": "model_input",
"modelWorkflow.run_Model.model_git_repository": "https://github.com/HopkinsIDD/flepiMoP.git",
"modelWorkflow.run_Model.model_output_folder": "model_output",
"modelWorkflow.run_Model.model_output_file_types": "[parquet]",
"modelWorkflow.run_Model.install_model_script": "./scripts/sh/flepimop/install_model.sh",
"modelWorkflow.run_Model.run_model_script": "./scripts/sh/flepimop/run_model.sh",
"modelWorkflow.run_Model.model_runtime_docker": "rocker/verse:latest",
"modelWorkflow.setup_os_script": "./scripts/sh/setup_os.sh",
"modelWorkflow.clone_repository_script": "./scripts/sh/clone_git_repository.sh",
"modelWorkflow.copy_cromwell_logs_script": "./scripts/sh/copy_cromwell_logs.sh",
"modelWorkflow.copy_model_output_script": "scripts/python/copy_model_output.py"
}
- 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.
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