build_bracken_database.pbs

#!/bin/bash
# This script builds a Bracken database from a Kraken2 database.
# Parameters: db (path to a Kraken database), len (read length), k (k-mer length), wd (working directory),
#             x (path to the 'bin' subdirectory in Kraken2's installation directory),
#             p (directory where Bracken is installed), mod (module name where conda/python is installed - optional),
#             con (name of the conda environment where Python is installed - optional)
# Example command: qsub -v "k=35,len=150,db=$HOME/database/kraken2/bacteria_220526,x=$HOME/anaconda3/envs/kraken2.1/bin,p=$HOME/bin/Bracken,mod=anaconda3/personal,con=kraken2.1,wd=$PWD" build_bracken_database.pbs
#
# Copyright (C) 2020-2023 Yu Wan <wanyuac@126.com>
# Licensed under the GNU General Public Licence version 3 (GPLv3) <https://www.gnu.org/licenses/>.
# Release: 2020; latest update: 4 Jan 2023

### Job configurations ###############
#PBS -N bracken-build
#PBS -l select=1:ncpus=8:mem=64gb:ompthreads=8
#PBS -l walltime=24:00:00
#PBS -j oe

if [ ! -z "$mod" ]; then
    echo "Loading environmental module $mod"
    module load $mod
fi

if [ ! -z "$con" ]; then
    echo "Activating Conda environment $con"
    source activate $con  # Some systems use 'source' instead of 'conda' to load an environment.
    # conda activate $con
fi

if [ -z "$k" ]; then
    echo "Waring: parameter 'k' is not specified, so k = 35 is used by default."
    k=35
fi

if [ -z "len" ]; then
    echo "Warning: parameter 'len' is not specified, so len = 100 is used by default."
    len=100
fi

if [ ! -f "$p/bracken-build" ]; then
    if [ -f "./bracken-build" ]; then
        p='.'
    else
        echo "Error: bracken-build is not found in directory $p"
        exit 1
    fi
fi

### Main ###############
cd $wd

if [ ! -z "$db" ]; then
    echo -e "Building a Bracken database (k-mer = $k, read length = $len) from $db using $NCPUS cores.\n"
    $p/bracken-build -k $k -l $len -d $db -x $x -t $NCPUS
else
    echo "Error: no Kraken2 database is specified for variable 'db'."
fi