inspect_kraken2_database.pbs

#!/bin/bash
# This script builds a custome Kraken database.
# Parameters: conda_module (module name for loading conda), env (conda environment), db (database name and path), wd (working directory), 
# Dependencies: conda (anaconda/miniconda), Kraken 2, PBS
# Example command: qsub -v "conda_module=anaconda3/personal,env=kraken2.1,db=bacteria_220526,wd=$PWD" ~/Kraken_toolkit/inspect_kraken2_database.pbs
#
# Copyright (C) 2020-2022 Yu Wan <wanyuac@126.com>
# Licensed under the GNU General Public Licence version 3 (GPLv3) <https://www.gnu.org/licenses/>.
# First release: 3 June 2022; latest update: 3 June 2022

### Job configurations ###############
#PBS -N kraken2-inspect
#PBS -l select=1:ncpus=8:mem=64gb:ompthreads=8
#PBS -l walltime=24:00:00
#PBS -j oe

if [ ! -z "$conda_module" ]; then
    module load $conda_module
fi

if [ ! -z "$env" ]; then  # Comment/uncomment the command 'source activate' or 'conda activate' for your HPC's setting
    source activate $env  # Includes an openmpi installation from bioconda
    # conda activate $env
fi

if [ -z "$db" ]; then
    echo "Warning: the Kraken2 database is not found."
    exit 1
fi

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

echo "Running kraken2-inspect with $NCPUS cores."
kraken2-inspect --db $db --threads $NCPUS > ${db}_summary.txt