The User executes a verified workflow on their local machine using its PID and local Conda installation. Complete System Preparation before proceeding.

1. Run the FDO Client¶

The FDO client automates the download, verification, and Snakemake execution steps.

1. Initiate Run: Execute the workflow using its PID and specify the local input directory.

   fdo-run-client 21.11152/workflow_A01 --input "C:\User\Data\RawSequences" --cores 4
   

2. Client Verification Steps:

   • Resolve PID: Query the MaRDI DOIP server to retrieve the storage URL and original checksum.
   • Download & Extract: Download the RO-Crate and extract it to a temporary working directory.
   • Verify Integrity: Calculate the checksum of the downloaded archive. Execution stops if it does not match the PID record.
   • Prepare: Map the user input directory into the Snakemake configuration.

3. Snakemake Execution: The client launches the Snakemake run command:

   snakemake -s /path/to/Snakefile --cores 4 --use-conda --conda-frontend mamba --config input_path="/path/to/input/data"
   

2. Reproducibility Across Platforms¶

Because the --use-conda flag is used:

• Snakemake reads the environment.yaml files from the downloaded RO-Crate.
• Mamba creates isolated environments with exact dependency versions compiled for the user's OS.
• The workflow runs identically across Windows, Linux, and macOS without requiring Docker or virtualization.