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Use HTTPS instead for plasmids, update path #529

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Use HTTPS instead for plasmids, update path #529

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10 changes: 6 additions & 4 deletions scripts/download_genomic_library.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ set -e # Stop on error
LIBRARY_DIR="$KRAKEN2_DB_NAME/library"
NCBI_SERVER="ftp.ncbi.nlm.nih.gov"
FTP_SERVER="ftp://$NCBI_SERVER"
HTTP_SERVER="https://$NCBI_SERVER"
RSYNC_SERVER="rsync://$NCBI_SERVER"
THIS_DIR=$PWD

Expand Down Expand Up @@ -61,15 +62,16 @@ case $library_name in
cd $LIBRARY_DIR/plasmid
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/
1>&2 echo -n "Downloading plasmid file manifest from FTP..."
wget -q --no-remove-listing --spider $FTP_SERVER/refseq/release/plasmid/
if [ -n "$KRAKEN2_PROTEIN_DB" ]; then
awk '{ print $NF }' .listing | perl -ple 'tr/\r//d' | grep '\.faa\.gz' > manifest.txt
else
awk '{ print $NF }' .listing | perl -ple 'tr/\r//d' | grep '\.fna\.gz' > manifest.txt
fi
cat manifest.txt | xargs -n1 -I{} wget -q $FTP_SERVER/genomes/refseq/plasmid/{}
cat manifest.txt | xargs -n1 -I{} gunzip -c {} > $library_file
1>&2 echo -n "Downloading plasmid files from HTTP..."
cat manifest.txt | xargs -I{} wget -q $HTTP_SERVER/refseq/release/plasmid/{}
cat manifest.txt | xargs -I{} gunzip -c {} > $library_file
rm -f plasmid.* .listing
scan_fasta_file.pl $library_file > prelim_map.txt
1>&2 echo " done."
Expand Down