Bash/run AutoMLST at main · janis0616/Bash · GitHub

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#!/usr/bin/env bash
#Pipeline for bacterial species identification and ANI using the tool AutoMLST
#Make sure you have a conda environment with the autoMLST dependencies (in the environment.yml file when you download autoMLST; it's easiest to just add to environment.yml and run: conda env create --file environment.yml)
#Run in directory with a sub-directory for each sample, containing the fasta file
#Output will be in output.tsv
#Edit paths as necessary

#First, activate Conda environment: conda activate automlst

for dir in */
do
	cd $dir
	printf "\n\nAutoMLST\n" >> output.tsv
	mkdir ./fasta/
	cp contigs.fasta ./fasta/contigs.fasta
	#ANI (autoMLST)
	python /home/mdungsmain/Janis/Programs/automlst/automlst.py ./fasta/ ./ -c 10 -ref /home/mdungsmain/Janis/Programs/automlst/refseqreduced.db -rd /home/mdungsmain/Janis/Programs/automlst/automlstrefs.tar.gz
	head -11 mash_distances.txt >> output.tsv
	cd ..
done