I would like to run lefse locally with conda. I have followed the tutorial, but when I run this line from the tutorial example,
$ lefse_format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
only a txt file opens with the following:
#!/bin/sh '''exec' C:/Users/Peter/anaconda3/envs/biobakery_env/bin/python "$0" "$@" ' ''' # -*- coding: utf-8 -*- import re import sys from lefse.lefse_format_input import format_input if __name__ == '__main__': sys.argv = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv) sys.exit(format_input())
What could be the problem? I couldn’t find any topic with a similar issue on the forum. I am working on windows with python 3.10.6.