I'm just starting with Mugsy for genome alignments and I have some trouble with the usage of Mugsy.
I installed it using bioconda and when I activate Mugsy with:
conda activate Mugsy it works because I can have access to the help page.
I'm using this command line:
mugsy --directory /data/output_mugsy --prefix mygenomes genome1.fasta genome2.fasta
but I have the following error message:
-directory must be a directory at /home/administrateur/miniconda3/envs/Mugsy/bin/mugsy line 235.
I tried to look online but unfortunately didn't find anything that helped me.. So If by chance, you have any idea on how I can fix this, please let me know!
Thank you in advance for your much appreciated help