diff --git a/bin/downloadKalamari.sh b/bin/downloadKalamari.sh index 0d5cd6c..71e72ea 100755 --- a/bin/downloadKalamari.sh +++ b/bin/downloadKalamari.sh @@ -41,39 +41,8 @@ if [[ ${KALAMARI_DEBUG:-} ]]; then grep -m 5 Legionella $TSV.tmp >> $TSV fi -function build_kraken1(){ - in_dir=$1 - DB=$2 - - rm -rvf $DB - mkdir -v $DB - cp -rv $tempdir/taxonomy $DB/ - find $in_dir -name '*.fasta' -exec kraken-build -db $DB \ - --add-to-library {} \; - kraken-build --db $DB --build --threads 1 - kraken-build --db $DB --clean - du -shc $DB - - echo "DONE. Set KRAKEN_DEFAULT_DB=$(realpath $DB)" -} - -function build_kraken2(){ - in_dir=$1 - DB=$2 - - rm -rvf $DB - mkdir -v $DB - cp -rv $tempdir/taxonomy $DB/ - find $in_dir -name '*.fasta' -exec kraken2-build -db $DB \ - --add-to-library {} \; - kraken2-build --db $DB --build --threads 1 - kraken2-build --db $DB --clean - du -shc $DB - echo "DONE. Set KRAKEN2_DEFAULT_DB=$(realpath $DB)" -} - perl $thisdir/downloadKalamari.pl $TSV \ - --outdir $tempdir/kalamari + --outdir $tempdir/kalamari --buffersize 100 rm -rf $outdir_prefix mkdir -v $outdir_prefix