bio-miga/miga

#!/bin/bash
# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
set -e
SCRIPT="project_stats"
# shellcheck source=scripts/miga.bash
. "$MIGA/scripts/miga.bash" || exit 1
DIR="$PROJECT/data/90.stats"

# Initialize
miga_start_project_step "$DIR"

# Execute doctor (bidirectional is checked in haai_distances)
echo "# Doctor"
miga doctor -P "$PROJECT" -t "$CORES" -v --ignore bidirectional

# Index taxonomy
echo "# Index taxonomy"
miga tax_index -P "$PROJECT" -i "miga-project.taxonomy.json" --ref --active

# Index metadata
echo "# Index metadata"
ruby -I "$MIGA/lib" \
  "$MIGA/utils/index_metadata.rb" "$PROJECT" "miga-project.metadata.db"

# Finalize
miga_end_project_step "$DIR"