module load hmmer/3.1b2
module load R/3.4.3
module load ncbi-blast/2.6.0
module load python/2.7.12
module load augustus/3.3

#Create a local copy of the augustus/3.3 config directory and then export the path to it. BUSCO writes to the config directory if you use genome mode, so you need a local copy.
export AUGUSTUS_CONFIG_PATH="/scratch/dsw0002/Augustus_config/config/"

#Usage: python <path/to/run_BUSCO.py -i <input.fasta> -o <output_directory_name> -l <path_to_BUSCO_db_of_interest> -m <genome, proteins, or transcriptome> -c <CPUs> --species <augustus_trained_closest_species>
for FILE in *genome.fa
do
	python ~/bin/busco/scripts/run_BUSCO.py -i $FILE -o $FILE -l /tools/funannotate-1.5.0/db/tetrapoda -m genome -c 10 --species human
done


