/lrgasp-challenge-3_manatee_benchmarking_workflow

Primary LanguageNextflow

LRGASP challenge 3 OpenEBench manatee workflow

The workflow used to run the LRGASP challenge 3 manatee docker in the OpenEBench VRE executor.

The repository includes several files:

  1. lrgasp-challenge-3_full_data folder: An example input dataset.
  2. config.json: The workflow configuration file containing various elements under arguments, such as the workflow's git repository, specific commit, community id, participant id, and the parameters for the challenges to compute.
  3. in_metadata.json: Defines the input files' directories. The file specifies the input files' detailed locations within the config.json.
  4. materalize-data.sh: Downloads the required datasets to pre-defined relative paths.
  5. materialize-containers.sh: Builds the necessary containers for the LRGASP workflow (not currently in use, directly downloads from Docker Hub instead).

Usage

  1. Install OpenEBench VRE executor and go to the tests folder
cd vre-process_nextflow-executor
source .py3Env/bin/activate
cd tests
  1. Clone the LRGASP manatee workflow repository and rename the folder to LRGASP_manatee
git clone https://github.com/TianYuan-Liu/lrgasp-challenge-3_manatee_benchmarking_workflow.git
mv lrgasp-challenge-3_manatee_benchmarking_workflow LRGASP_manatee
  1. Materialize both the containers and datasets needed by the LRGASP test:
cd LRGASP_manatee
bash ./materialize-data.sh
  1. Run the tests from LRGASP_manatee example
cd ../..
./test_VRE_NF_RUNNER.sh LRGASP_manatee