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#!/bin/bash
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
# Build the standard Kraken database
# Designed to be called by kraken_build
set -u # Protect against uninitialized vars.
set -e # Stop on error
set -o pipefail # Stop on failures in non-final pipeline commands
protein_flag=""
if [ -n "$KRAKEN2_PROTEIN_DB" ]; then
protein_flag="--protein"
fi
masking_flag=""
if [ -z "$KRAKEN2_MASK_LC" ]; then
masking_flag="--no-mask"
fi
ftp_flag=""
if [ -n "$KRAKEN2_USE_FTP" ]; then
ftp_flag="--use-ftp"
fi
kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library archaea $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library bacteria $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library viral $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library plasmid $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library human --no-mask $protein_flag $ftp_flag
if [ -z "$KRAKEN2_PROTEIN_DB" ]; then
kraken2-build --db $KRAKEN2_DB_NAME --download-library UniVec_Core $masking_flag $ftp_flag
fi
kraken2-build --db $KRAKEN2_DB_NAME --build --threads $KRAKEN2_THREAD_CT \
--minimizer-len $KRAKEN2_MINIMIZER_LEN \
--kmer-len $KRAKEN2_KMER_LEN \
--minimizer-spaces $KRAKEN2_MINIMIZER_SPACES \
$protein_flag
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