Tutorial on submitting a BUSCO job with slurm.

Here we see how to run the bioinformatics tool BUSCO on a de novo genome file. The code used in the video is listed below. Feel free to subscribe if you found this video helpful!
#genomes.txt
Coprinus_1A;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/;/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/fasta/scaffolds.fasta
#BUSCO.sh
#!/bin/bash
#SBATCH --partition=all.q
#SBATCH -J BUSCO_Coprinus # Set the job name
#SBATCH -o BUSCO_Coprinus_output # Output files for stdout and stderr
#SBATCH -e BUSCO_Coprinus_error # Error files
MYFILE='/nfs7/McMurtrey_Lab/de_novo/BUSCO/CAP1/genomes.txt'
for LINE in `cat ${MYFILE}`; do
ELEMENT1=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $1}'`
echo "ELEMENT1 is: ${ELEMENT1}"
ELEMENT2=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $2}'`
echo "ELEMENT2 is: ${ELEMENT2}"
ELEMENT3=`echo ${LINE} | awk 'BEGIN{FS=";"}{print $3}'`
echo "ELEMENT3 is: ${ELEMENT3}"
conda init
conda activate /home/bpp/mcmurtrs/nfs7/conda/miniconda3
CMD=" busco -f -i ${ELEMENT2} -l basidiomycota_odb10 -m genome -o ${ELEMENT1}_busco "
echo $CMD
eval $CMD
echo -n "Finished running BUSCO!"
done