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Fixed download error of plasmids (DerrickWood#543)
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kmavrommatis authored Jan 12, 2024
1 parent acc2248 commit f4aa485
Showing 1 changed file with 5 additions and 1 deletion.
6 changes: 5 additions & 1 deletion scripts/download_genomic_library.sh
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,11 @@ case $library_name in
rm -f library.f* plasmid.*
## This is staying FTP only D/L for now
1>&2 echo -n "Downloading plasmid files from FTP..."
wget -q --no-remove-listing --spider $FTP_SERVER/genomes/refseq/plasmid/
#wget -q --no-remove-listing --spider $FTP_SERVER/genomes/refseq/plasmid/
curl -s $FTP_SERVER/genomes/refseq/plasmid/ \
| perl -nle 'print "$1" while (/<a\s+href\s*=\s*"([^"]+.gz)"/g)' \
| sort -u \
> .listing
if [ -n "$KRAKEN2_PROTEIN_DB" ]; then
awk '{ print $NF }' .listing | perl -ple 'tr/\r//d' | grep '\.faa\.gz' > manifest.txt
else
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