buildFivProject.glue

  # Build species-level extension projects

  # Feline lentiviruses
  project lentivirus

    # Import sources
    run file glue/build/extension/feline/sourcesFeline.glue

    # Define extension references
    run file glue/build/extension/feline/referencesFeline.glue

    # Extract and import isolate data for extension sequences
    run file glue/build/extension/feline/importIsolateDataFeline.glue

	# Import alignments
	run file glue/build/extension/feline/alignmentFeline.glue

	# Add extension set sequences constrained alignment tree
	run file glue/build/extension/feline/alignmentTreeFeline.glue
    run file glue/build/extension/feline/alignmentTreeFivGenotyping.glue

	# Compute alignments
	run file glue/build/extension/feline/createAlignmentsFeline.glue

    # Derive constrained genotyping alignment from unconstrained
    #
    
	# Record feature presence
	#run file glue/build/extension/feline/recordFeaturePresenceFeline.glue

    # Import reference phylogeny
    run file glue/build/extension/feline/importGenotypingPhylogenyFiv.glue

	# Validate
	validate

	exit