update_blat

#!/bin/bash

pkill gfServer || :

echo "downloading dbDb spreadsheet from https://spreadsheets.google.com/feeds/download/spreadsheets/Export?key="$DBDBID"&hl=en&exportFormat=tsv"
curl -sL "https://spreadsheets.google.com/feeds/download/spreadsheets/Export?key="$DBDBID"&hl=en&exportFormat=tsv" | \
  tr -d "\r" | \
  awk -F '\t' -v header=active  '
  BEGIN {
    split(header,cols,",")
  }
  {
    if(NR==1){
      for (i=1; i<=NF; i++){cols[$i]=i}
      print $0
    }
    if(NR>1 && $cols["active"]==1){
      print $0
    }
  }' OFS='\t' > /tmp/dbDb.tsv
echo "found" $(grep -v "^name" /tmp/dbDb.tsv | wc -l) "activated genomes"

echo "processing genomes"
cols=$(head -n 1 /tmp/dbDb.tsv)
tail -n+2 /tmp/dbDb.tsv | while IFS=$'\t' read -r $cols
do
  if [ $active -eq 1 ]; then
    if [[ $(hostname) == $nBlatHost ]] && [[ $nBlatPort != "NA" ]]; then
      echo "starting nucleotide blat service for $name"
      gfServer -tileSize=7 -canStop start $(hostname).$DOMAIN $nBlatPort -stepSize=5 $nibPath/genome.2bit &
    fi

    if [[ $(hostname) == $pBlatHost ]] && [[ $pBlatPort != "NA" ]]; then
      echo "starting protein blat service for $name"
      gfServer -trans -canStop start $(hostname).$DOMAIN $pBlatPort $nibPath/genome.2bit &
    fi
  fi
done