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update NCBI URLs to use HTTPS for taxonomy data #198

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update NCBI URLs to use HTTPS for taxonomy data #198

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4 changes: 2 additions & 2 deletions KronaTools/updateTaxonomy.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ function fetch

echo "Fetching $description$depDesc..."

curl$timestring -s -R --retry 1 -o $name ftp://ftp.ncbi.nih.gov/pub/taxonomy/$prefix/$name
curl$timestring -s -R --retry 1 -o $name https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/$prefix/$name
return=$?

if [ $return == "23" ]
Expand All @@ -129,7 +129,7 @@ function fetch
then
echo " Fetching checksum..."

curl -s -R --retry 1 -o $name.md5 ftp://ftp.ncbi.nih.gov/pub/taxonomy/$prefix/$name.md5
curl -s -R --retry 1 -o $name.md5 https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/$prefix/$name.md5
checksum=$($MD5 $name | cut -d ' ' -f 1)
checksumRef=$(cut -d ' ' -f 1 $name.md5)
rm $name.md5
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