Permalink
Browse files

Fix downloads for nt/nr and UniVec

  • Loading branch information...
DerrickWood committed Sep 17, 2018
1 parent 77d8dd1 commit bc14b1318f44359d6aa0a0b6e014bbe91a3a8fcc
Showing with 5 additions and 5 deletions.
  1. +5 −5 scripts/download_genomic_library.sh
@@ -86,8 +86,8 @@ case $library_name in
mkdir -p $LIBRARY_DIR/$library_name
cd $LIBRARY_DIR/$library_name
rm -f $library_name.gz
1>&2 echo -n "Downloading $library_name database from FTP..."
download_file $FTP_SERVER/blast/db/FASTA/$library_name.gz
1>&2 echo -n "Downloading $library_name database from server... "
download_file "/blast/db/FASTA/$library_name.gz"
1>&2 echo "done."
1>&2 echo -n "Uncompressing $library_name database..."
gunzip $library_name.gz
@@ -106,12 +106,12 @@ case $library_name in
fi
mkdir -p $LIBRARY_DIR/$library_name
cd $LIBRARY_DIR/$library_name
1>&2 echo -n "Downloading $library_name data from FTP..."
download_file $FTP_SERVER/pub/UniVec/$library_name
1>&2 echo -n "Downloading $library_name data from server... "
download_file "/pub/UniVec/$library_name"
1>&2 echo "done."
# 28384: "other sequences"
special_taxid=28384
1>&2 echo -n "Adding taxonomy ID of $special_taxid to all sequences..."
1>&2 echo -n "Adding taxonomy ID of $special_taxid to all sequences... "
sed -e "s/^>/>kraken:taxid|$special_taxid|/" $library_name > library.fna
scan_fasta_file.pl library.fna > prelim_map.txt
1>&2 echo "done."

0 comments on commit bc14b13

Please sign in to comment.