diff --git a/bin/downloadKalamari.sh b/bin/downloadKalamari.sh index db150e0..6f4ba26 100755 --- a/bin/downloadKalamari.sh +++ b/bin/downloadKalamari.sh @@ -6,6 +6,7 @@ if [[ "$1" =~ -h ]]; then echo "Usage: $0 " echo " Downloads the standard chromosomes and plasmids for Kalamari" echo " from source and formats the kraken1 and kraken2 databases" + echo " Debug with env variable KALAMARI_DEBUG=1" exit 0 fi @@ -28,10 +29,14 @@ cat $thisdir/../src/plasmids.tsv >> $TSV cp -rv $thisdir/../src/taxonomy $tempdir/taxonomy # Debug with `KALAMARI_DEBUG=1 downloadKalamari.sh` -if [[ ${KALAMARI_DEBUG:+1} ]]; then - echo "DEBUG was set and so just downloading a few entries" >&2 - mv $TSV $TSV.tmp && \ - head -n 10 $TSV.tmp > $TSV +if [[ ${KALAMARI_DEBUG:-} ]]; then + echo "DEBUG" >&2 + mv $TSV $TSV.tmp + head -n 1 $TSV.tmp > $TSV + grep -m 5 Salmonella >> $TSV + grep -m 5 Listeria >> $TSV + grep -m 5 Escherichia>> $TSV + grep -m 5 Campylobacter >> $TSV fi function build_kraken1(){