buildPrimateLentivirusExtension.glue

    # Build species-level extension projects

    # Primate lentiviruses

     project lentivirus

        # Create modules
        run file glue/build/extension/primate/modulesPrimate.glue

        # Import sources
        run file glue/build/extension/primate/sourcesPrimate.glue

        # Define additional features (HIV-1)
        run file glue/build/extension/primate/hivFeatures.glue

        # Define extension references
        run file glue/build/extension/primate/referencesPrimate.glue

        # Attach feature locations to the reference sequences
        run file glue/build/extension/primate/explicitFeatureLocationsPrimate.glue

        # Extract and import isolate data for extension sequences
        run file glue/build/extension/primate/importIsolateDataPrimate.glue

        # Import the root alignment for the HIV-1 clade
        run file glue/build/extension/primate/createHivRootAlignment.glue

        # Add extension set sequences constrained alignment tree
        run file glue/build/extension/primate/alignmentTreePrimate.glue

        # Record feature presence
        #run file glue/build/extension/primate/recordFeaturePresencePrimate.glue

        # Attach feature locations to the reference sequences
        #run file glue/core/hivVariations.glue

        # Validate
        validate

        exit