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InvokeProkka.sh
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InvokeProkka.sh
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# This script uses prokka to re-annotate genomes.
# Create by Mingzhi Lin ([email protected]).
# Usage:
# bash InvokeProkka.sh <accession list file> <genome folder> <prokka output folder>
# It requires
# (1) https://github.com/tseemann/prokka
# (2) https://www.gnu.org/software/parallel
# If you are using NYU HPC, ask [email protected] for help.
function invoke_prokka() {
genome=$1
workspace=$2
genomefile=$3/$genome/${genome}_genomic.fna
prokka --cpus 1 --force --centre X --compliant --outdir ${workspace}/${genome} --prefix ${genome} ${genomefile} --quiet
}
export -f invoke_prokka
accessionlistfile=$1
genomefolder=$2
prokkafolder=$3
echo "Inovking Prokka to re-annotate genomes..."
parallel invoke_prokka {} $prokkafolder $genomefolder :::: $accessionlistfile
echo "Completed running Prokka, saved results to ${prokkafolder}"