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buildCoreProject.glue
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buildCoreProject.glue
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delete project hepadnaviridae
create project hepadnaviridae "GLUE project for the Hepadnaviridae" --minVersion 1.1.65
schema-project hepadnaviridae
run file glue/build/hepadnaSchemaExtensions.glue
exit
# Build core project
project hepadnaviridae
# Load project settings
run file glue/build/hepadnaProjectSettings.glue
# Create modules
run file glue/build/hepadnaModules.glue
# Import sequence data
run file glue/build/importSources.glue
# Import sequence-associated "side-data" for core project reference sequences
run file glue/build/hepadnaImportData.glue
# Define genome features
run file glue/build/hepadnaFeatures.glue
# Create reference sequences
run file glue/build/hepadnaMasterReferences.glue
# Apply rotations
run script glue/build/hepadnaRefseqsApplyRotations.js
# Add feature locations
run file glue/build/hepadnaExplicitFeatureLocations.glue
run file glue/build/nackednaExplicitFeatureLocations.glue
# Import alignments
run file glue/build/hepadnaAlignments.glue
# Define alignment tree
run file glue/build/hepadnaAlignmentTree.glue
# Compute alignments (for constrained alignments that include taxa absent from imported, unconstrained alignment
run file glue/build/hepadnaComputeAlignments.glue
# Record feature coverage in alignments
run file glue/build/hepadnaRecordFeaturePresence.glue
# Define variations
run file glue/build/hepadnaVariations.glue
# Validate
validate
exit