chikvBaseProject.glue

delete project chikv

create project chikv "A GLUE project for chikungunya virus (CHIKV)" --minVersion 1.1.107

run file glue/chikvSchemaExtensions.glue
 
project chikv

  run file glue/chikvProjectSettings.glue
  run file glue/chikvModules.glue

  # Set up ISO countries  
  run file glue/m49_countries/populateM49All.glue

  # NCBI refseqs -- taxa in the reference phylogeny, plus the RefSeq master reference and a numbering reference
  import source sources/ncbi-refseqs
 
  # Link sequence table entries to isolate table
  run script glue/chikvLoadIsolateData.js 
  
  # Populate refseq + outgroup metadata from GenBank XML
  module chikvGenbankXmlPopulator populate -w "source.name = 'ncbi-refseqs'"

  # Load tabular data
  module chikvSideDataImporter
    populate -f tabular/chikv_reference_data.tsv
    exit

  # Define references
  run file glue/chikvReferences.glue

  # Import unconstrained alignment
  run file glue/chikvUnconstrainedAlignments.glue

  # Define alignment tree
  run file glue/chikvAlignmentTree.glue

  # Define features
  run file glue/chikvFeatures.glue
  
  # Define feature locations on master references
  run file glue/chikvExplicitFeatureLocations.glue
  
  # inherit feature locations across other references
  run script glue/chikvRefseqsInheritFeatureLocations.js
  run script glue/chikvValidateRefseqFeatureLocations.js

  # import the reference phylogeny into the alignment tree
  run file glue/chikvImportPhylogeny.glue
  
  # Validate
  validate

exit