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buildDengueProject.glue
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buildDengueProject.glue
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delete project dengue
create project dengue "A GLUE project for Dengue virus (DENV)" --minVersion 1.1.107
run file glue/denvSchemaExtensions.glue
project dengue
run file glue/denvProjectSettings.glue
run file glue/denvModules.glue
# Set up M49 standard for country & region data
run file glue/m49_countries/populateM49All.glue
# Define dengue virus features
run file glue/denvFeatures.glue
# Import sources
run file glue/denvImportSources.glue
# Import data
run file glue/denvImportData.glue
# Define references
run file glue/references/denvMasterReferences.glue
run file glue/references/denvGenotypeReferences.glue
run file glue/references/denv1LineageReferences.glue
run file glue/references/denv2LineageReferences.glue
run file glue/references/denv3LineageReferences.glue
run file glue/references/denv4LineageReferences.glue
# Compute the unconstrained MSAs containing only genotype reference sequences
run file glue/denvCreateUncMsas.glue
run file glue/denvComputeUncMsas.glue
# Define alignment tree
run file glue/denvAlignmentTree.glue
# Derive constrained MSAs from unconstrained
run file glue/denvDeriveConstrainedMsas.glue
# Compute reference phylogenies
#run file glue/denvComputeRefPhylogenies.glue
# Prepare reference phylogenies
run file glue/denvPrepareRefPhylogenies.glue
# Import reference phylogenies
run file glue/denvImportPhylogenies.glue
# Validate
validate
exit