System Preparation

Previous Next

The following one-time setup is required per machine before running any Conda-based Snakemake workflow. Install all four components for your operating system.

  1. Mamba/Conda: Install Miniforge (recommended):

    • Download from conda-forge.github.io/miniforge
    • Run the .exe installer and select "Add to PATH" during installation
    • Verify: Open PowerShell or CMD and run mamba --version

  2. Python: Comes bundled with Miniforge (Python 3.9+ recommended).

    • Verify: python --version

  3. Snakemake: Install the Snakemake engine in a dedicated environment:

    mamba create -n snakemake -c conda-forge -c bioconda snakemake
mamba activate snakemake

  4. FDO Client: Install your custom command-line client:

    • Download the latest fdo-client-windows-x64.exe CLI from [https://github.com/MaRDI4NFDI/mardi_doip_server]
    • Rename to fdo-run-client.exe and move to a directory in your PATH (e.g., C:\Tools\)
    • Verify: fdo-run-client --version

  1. Mamba/Conda: Install Miniforge (recommended): 

    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh
# Follow prompts, then reload shell: source ~/.bashrc

    • Verify: mamba --version

  2. Python: Comes bundled with Miniforge (Python 3.9+ recommended).

    • Verify: python --version

  3. Snakemake: Install the Snakemake engine in a dedicated environment:

    mamba create -n snakemake -c conda-forge -c bioconda snakemake
mamba activate snakemake

  4. FDO Client: Install your custom command-line client: 

    wget https://github.com/MaRDI4NFDI/mardi_doip_server/releases/latest/download/fdo-client-linux-x64 -O fdo-run-client
chmod +x fdo-run-client
sudo mv fdo-run-client /usr/local/bin/

    • Verify: fdo-run-client --version

  1. Mamba/Conda: Install Miniforge (recommended):

    • For Intel Macs: Download Miniforge3-MacOSX-x86_64.sh
    • For Apple Silicon (M1/M2/M3): Download Miniforge3-MacOSX-arm64.sh
    • Both available at conda-forge.github.io/miniforge
    • Run: bash Miniforge3-MacOSX-*.sh and follow prompts
    • Reload shell: source ~/.zshrc (or ~/.bash_profile for older macOS)
    • Verify: mamba --version

  2. Python: Comes bundled with Miniforge (Python 3.9+ recommended).

    • Verify: python --version

  3. Snakemake: Install the Snakemake engine in a dedicated environment:

    mamba create -n snakemake -c conda-forge -c bioconda snakemake
mamba activate snakemake

  4. FDO Client: Install your custom command-line client: 

    # For Intel Macs
curl -L https://github.com/MaRDI4NFDI/mardi_doip_server/releases/latest/download/fdo-client-macos-x64 -o fdo-run-client

# For Apple Silicon (M1/M2/M3)
curl -L https://github.com/MaRDI4NFDI/mardi_doip_server/releases/latest/download/fdo-client-macos-arm64 -o fdo-run-client

chmod +x fdo-run-client
sudo mv fdo-run-client /usr/local/bin/

    • Verify: fdo-run-client --version

Next: Creating a Workflow FDO

Overview Creating a Workflow FDO