setenv PERL5LIB $gbl/lib:${PERL5LIB}

echo '# 4a. create primary genome GFF db for Gbrowse (Lucene adaptor)'
echo '# lucene/${dp}_caf1'

$gbl/bin/lu_bulk_load_gff.pl -create -java $gbl/lib/java  \
  -data lucene/${dp}_caf1 \
  -fasta $scd/${dpid}.fa.gz \
  $scd/${dp}-chromosomes.gff $scd/${dp}-scaffolds.gff \
  $scd/${dp}-markers.gff.gz  \
  $scd/${dp}-dmel-algn.gff.gz \
  $scd/${dp}-dros-micsat.gff.gz \
  $scd/${dp}-prot9-strong2.gff.gz \
  >& log.lu.$dpid &

echo '# 4b. create genome annotation/prediction GFF db for Gbrowse (Lucene adaptor)'
echo '# lucene/${dp}_caf1an4'

$gbl/bin/lu_bulk_load_gff.pl -create -java $gbl/lib/java \
  -data lucene/${dp}_caf1an4 \
  $sc/caf1a/dgil/${dp}prot9-hsp.gff.gz \
  $sc/caf1a/oliv/${dp}.caf1.gff.gz \
  $sc/caf1a/ncbi/${dp}_caf1_NCBI_GNO.gff.gz \
  $sc/caf1a/pach/${dp}_CAF1.gff.gz \
  $sc/caf1a/oxfd/${dp}_caf1.gff.gz \
  $sc/caf1a/rgui/geneidv1.2/${dp}_caf1.gff3.gz \
  $sc/caf1a/bren/${dp}_caf1.gff3.gz \
  $sc/caf1a/dgil/${dp}_caf1_DGIL.gff.gz \
  $sc/caf1a/dgil/${dp}_caf1_DGIL_SNO.gff.gz \
  $sc/caf1a/eise/genemapper/${dp}.gff3.gz \
  $sc/caf1a/eise/genewise/${dp}.gff3.gz \
  $sc/caf1a/eise/exonerate/${dp}.gff3.gz \
  $sc/caf1a/batz/contrast_na/${dp}.gff.gz \
  $sc/caf1c/umd/jigsaw-20060707/${dp}.gff3.gz  \
  $sc/caf1c/eise/glean/allsets/gff3/${dp}.gff3.gz  \
  >& log.lu${dp}_an4 &