bio-miga/miga

#!/bin/bash
# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
set -e
SCRIPT="distances"
# shellcheck source=scripts/miga.bash
. "$MIGA/scripts/miga.bash" || exit 1
cd "$PROJECT/data/09.distances"

# Initialize
miga date > "$DATASET.start"

# Check quality
MARKERS=$(miga ls -P "$PROJECT" -D "$DATASET" --markers \
  | wc -l | awk '{print $1}')
if [[ "$MARKERS" -eq "1" ]] ; then
  miga stats -P "$PROJECT" -D "$DATASET" -r essential_genes --compute-and-save
  inactive=$(miga ls -P "$PROJECT" -D "$DATASET" -m inactive | cut -f 2)
  [[ "$inactive" == "true" ]] && exit
fi

# Run distances
ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"

# Finalize
fastaai=no
aai=no
ani=no
blast=no
blat=no
diamond=no
fastani=no
if [[ ! -s "${DATASET}.empty" ]] ; then
  case $(miga option -P "$PROJECT" -k haai_p) in
    fastaai)
      fastaai=yes
      ;;
    diamond)
      diamond=yes
      aai=yes
      ;;
    blast)
      blast=yes
      aai=yes
      ;;
  esac

  case $(miga option -P "$PROJECT" -k aai_p) in
    diamond)
      diamond=yes
      aai=yes
      ;;
    blast)
      blast=yes
      aai=yes
      ;;
  esac

  case $(miga option -P "$PROJECT" -k ani_p) in
    blast)
      blast=yes
      ani=yes
      ;;
    blat)
      blat=yes
      ani=yes
      ;;
    fastani)
      fastani=yes
      ;;
  esac
fi


miga date > "${DATASET}.done"
cat <<VERSIONS \
  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
=> MiGA
$(miga --version)
$(
  if [[ "$fastaai" == "yes" ]] ; then
    echo "=> FastAAI"
    fastaai version 2>&1 | perl -pe 's/.*=//'
  fi
)
$(
  if [[ "$fastani" == "yes" ]] ; then
    echo "=> FastANI"
    fastANI --version 2>&1 | grep . | perl -pe 's/^version //'
  fi
)
$(
  if [[ "$aai" == "yes" ]] ; then
    echo "=> Enveomics Collection: aai.rb"
    aai.rb --version 2>&1 | perl -pe 's/.*: //'
  fi
)
$(
  if [[ "$ani" == "yes" ]] ; then
    echo "=> Enveomics Collection: ani.rb"
    ani.rb --version 2>&1 | perl -pe 's/.*: //'
  fi
)
$(
  if [[ "$blast" == "yes" ]] ; then
    echo "=> NCBI BLAST+"
    blastp -version 2>&1 | tail -n 1 | perl -pe 's/.*: blast //'
  fi
)
$(
  if [[ "$blat" == "yes" ]] ; then
    echo "=> BLAT"
    blat 2>&1 | head -n 1 | perl -pe 's/.* v\. //' | perl -pe 's/ fast .*//'
  fi
)
$(
  if [[ "$diamond" == "yes" ]] ; then
    echo "=> Diamond"
    diamond --version 2>&1 | perl -pe 's/^diamond version //'
  fi
)
VERSIONS