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Updated kraken2-build to allow symlinks in the library directory #603

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Updated kraken2-build to allow symlinks in the library directory #603

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5ae9c27
Update build_kraken2_db.sh
oracle5th Jun 20, 2022
adf944a
Update build_kraken2_db.sh
oracle5th Jun 20, 2022
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6 changes: 3 additions & 3 deletions scripts/build_kraken2_db.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ function report_time_elapsed() {
}

function list_sequence_files() {
find library/ '(' -name '*.fna' -o -name '*.faa' ')' -print0
find -L library/ '(' -name '*.fna' -o -name '*.faa' ')' -print0
}

start_time=$(get_current_time)
Expand Down Expand Up @@ -66,14 +66,14 @@ fi

echo "Creating sequence ID to taxonomy ID map (step 1)..."
if [ -d "library/added" ]; then
find library/added/ -name 'prelim_map_*.txt' | xargs cat > library/added/prelim_map.txt
find -L library/added/ -name 'prelim_map_*.txt' | xargs cat > library/added/prelim_map.txt
fi
seqid2taxid_map_file=seqid2taxid.map
if [ -e "$seqid2taxid_map_file" ]; then
echo "Sequence ID to taxonomy ID map already present, skipping map creation."
else
step_time=$(get_current_time)
find library/ -maxdepth 2 -name prelim_map.txt | xargs cat > taxonomy/prelim_map.txt
find -L library/ -maxdepth 2 -name prelim_map.txt | xargs cat > taxonomy/prelim_map.txt
if [ ! -s "taxonomy/prelim_map.txt" ]; then
echo "No preliminary seqid/taxid mapping files found, aborting."
exit 1
Expand Down