Mugsy error -directory must be a directory

Question

[A_heath]

Hi all,

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

Audrey

[Jean-Karim Heriche]

See this previous post. In short, did you read the whole error message and did you set MUGSY_INSTALL in mugsyenv.sh?

[A_heath]

Thank you for your reply. Yes, i've aldready edited the file mugsyenv.sh:

#!/bin/sh
export MUGSY_INSTALL=/home/administrateur/Téléchargements/mugsy_x86-64-v1r2.2/mugsy
export PATH=$PATH:$MUGSY_INSTALL:$MUGSY_INSTALL/mapping
export PERL5LIB=$MUGSY_INSTALL/perllibs
#For testing TBA
#export PATH=$PATH:$MUGSY_INSTALL/../../multiz-tba/trunk/

But I still have the same issue

[GenoMax]

Did you do the following after editing the file as suggested by @h.mon in thread @Jean-Karim linked?

source mugsyenv.sh

[A_heath]

Yes, I did that too. In my Ubuntu terminal, I have this:

(Mugsy) administrateur:~$

and when I do:

(Mugsy) administrateur:~$ mugsy -h

I have the help instructions

So I don't know where the issue is ...

[GenoMax]

Does /data/output_mugsyexist?

[A_heath]

No it doesn't exist. Where should I create this directory?

[GenoMax]

Since you are indicating that as the location for the output (with --directory) I guess you should make it in that same location.