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buildCoreProject.glue
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buildCoreProject.glue
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delete project flu
create project flu "A GLUE project for influenzaviruses" --minVersion 1.1.41
run file glue/build/core/fluSchemaExtensions.glue
project flu
# load project settings
run file glue/build/core/projectSettings.glue
# create modules
run file glue/build/core/fluModules.glue
# Define genome features
run file glue/build/core/fluFeaturesNonCoding.glue
run file glue/build/core/fluFeaturesCoding.glue
# Import sequences
run file glue/build/core/fluImportSources.glue
# Import sequence-associated data
run file glue/build/core/fluLoadSequenceData.glue
# Import isolate data and link to imported sequences
run script glue/build/core/fluLoadIsolateDataNcbiRefseqs.js
# Define reference sequences
run file glue/build/core/fluReferences.glue
# Define feature locations on master reference sequences
run file glue/build/core/fluFeatureLocations.glue
# Import alignments
run file glue/build/core/fluLoadUnconstrainedAlignmentsSpecies.glue
# Define constrained alignment tree
run file glue/build/core/fluAlignmentTree.glue
# Derive constrained alignments from unconstrained alignments
run file glue/build/core/fluDeriveConstrainedMsasSpecies.glue
# Compute MSAs
run file glue/build/core/fluComputeAlignmentsIbv.glue
run file glue/build/core/fluComputeAlignmentsIav.glue
# Import phylogenies
#run file glue/build/core/iavImportPhylogenies.glue
#run file glue/build/core/ibvImportPhylogenies.glue
run file glue/build/core/icvImportPhylogenies.glue
run file glue/build/core/idvImportPhylogenies.glue
# Validate
validate
# Extension projects
#run file glue/build/extension/iav/buildIavExtension.glue
#run file glue/build/extension/ibv/buildIbvExtension.glue
#run file glue/build/extension/icv/buildIcvExtension.glue
#run file glue/build/extension/idv/buildIdvExtension.glue
exit