Option for the required software path

rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

GNU General Public License v3.0

306 stars 28 forks source link

Option for the required software path #74

Closed ASUQ closed 4 months ago

ASUQ commented 5 months ago

I am using Trycycler from a conda environment and faced

Error: unable to determine Mash version - make sure that Mash is correctly installed, then try again.

while running trycycler cluster. Could you add the option for the required software as you did in Unicycler?

rrwick commented 4 months ago

Sorry, but I'm probably not going to make any big changes to Trycycler going forward, as I'm working on a new tool which will replace Trycycler.

Do I correctly understand that you have Mash but not in your PATH variable, so Trycycler can't find it? If so, I think the easiest solutions would be one of the following:

Copy the mash executable to somewhere in your PATH, e.g. /usr/local/bin.
Temporarily add Mash's path to your PATH variable before running Trycycler: export PATH=/path/to/mash_dir/:"$PATH"

Do either of those work?

Ryan

ASUQ commented 4 months ago

Thanks for the reply, Ryan

It seems that mash is not correctly installed via the conda environment. I got the error when running trycycler cluster.

Error: unable to determine Mash version - make sure that Mash is correctly installed, then try again.

After installing Mash from https://github.com/marbl/Mash and adding into the path (export PATH=/path/to/mash_dir/:"$PATH"), it worked!

rrwick commented 4 months ago

Glad to hear it!