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Make build db compatible for OS X #58

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Make build db compatible for OS X #58

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13 changes: 11 additions & 2 deletions scripts/build_kraken_db.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,11 @@ else
# Estimate hash size as 1.15 * chars in library FASTA files
if [ -z "$KRAKEN_HASH_SIZE" ]
then
KRAKEN_HASH_SIZE=$(find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -printf '%s\n' | perl -nle '$sum += $_; END {print int(1.15 * $sum)}')
if [[ $(uname) == "Darwin" ]]; then
KRAKEN_HASH_SIZE=$(find library/ -name '*.ffn' -ls | awk '{print $7}' | perl -nle '$sum += $_; END {print int(1.15 * $sum)}')
else
KRAKEN_HASH_SIZE=$(find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -printf '%s\n' | perl -nle '$sum += $_; END {print int(1.15 * $sum)}')
fi
echo "Hash size not specified, using '$KRAKEN_HASH_SIZE'"
fi

Expand Down Expand Up @@ -104,7 +108,12 @@ else
echo "Skipping step 2, database reduction already done."
else
start_time1=$(date "+%s.%N")
kdb_size=$(stat -c '%s' database.jdb)
if [[ $(uname) == "Darwin" ]]; then
kdb_size=$(stat -f '%z' database.jdb)
else
kdb_size=$(stat -c '%s' database.jdb)
fi

idx_size=$(echo "8 * (4 ^ $KRAKEN_MINIMIZER_LEN + 2)" | bc)
resize_needed=$(echo "scale = 10; ($kdb_size+$idx_size)/(2^30) > $KRAKEN_MAX_DB_SIZE" | bc)
if (( resize_needed == 0 ))
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6 changes: 5 additions & 1 deletion scripts/upgrade_db.sh
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Expand Up @@ -70,7 +70,11 @@ then
exit 1
fi

idx_size=$(stat -c '%s' database.idx)
if [[ $(uname) == "Darwin" ]]; then
idx_size=$(stat -f '%z' database.idx)
else
idx_size=$(stat -c '%s' database.idx)
fi
# Calculate minimizer length based on existing index size
minimizer_len=$(perl -le 'print int(log(shift() / 8 - 2) / log(4))' $idx_size)

Expand Down