Installing BRAKER3 with GENEMARK configured on a local Galaxy server

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1

same problem for me! (this is a local galaxy-install (24.1) on ubuntu noble which otherwise runs nicely).

What I did:
gmes-folder placed at /opt/gmes
path exported: export GENEMARK_PATH=/opt/ (previous attempt: export GENEMARK_PATH=/opt/gmes did also not work)
finally also made a symbolic link to the folder: ln -s /opt/gmes/ /gmes/
license is copied to home folder of user “galaxy”
Result is always the same error message: Braker3 fails …
I really have no idea.
Thank you for any advice/help
Felix

2

The README file here has all of the configuration that I know about. → https://toolshed.g2.bx.psu.edu/repository?repository_id=36c87739f9e2cecf

This part doesn’t seem to match:

You should also copy a valid GeneMark license (from GeneMark™ download) in test-data/gm_key_64

Unless that is what you did? And galaxy has permissions to read that file?

You can share that and the other exact details called out in the RM, and we can see if someone more experienced with doing this configuration on a local has time to review and double check, then offer any advice.

Let’s start there, thanks!

3

Hello Jenna,

i copied the gm_key_64 to ../galaxy/test-data/ and checked the path variable, but braker3 is still not working.

At least there is no difference between this and former error messages:

galaxy@felixVM:~/git/galaxy$ env | grep GEN

GENEMARK_PATH=/opt/

4

Hi @felix

Hopefully you have solved this but if not, I think you are going to need to reach out to the tool developer to help with the troubleshooting. This is where to log an issue → GitHub · Where software is built. This is one example where the container needed a particular JAVA configuration: GitHub · Where software is built

The only other thing I can think of that the key is not in the /galaxy folder at the top level. Are am I misunderstanding this? Maybe you already tried both ways. Are the permissions set so that the galaxy user can read everything in the /opt folder, too? Are you running in the container?

We can also try asking some of the people who were involved with prior configuration corrections and one of the devs at this forum. Ping @abretaud or maybe @bjoern.gruening

And let’s cross-post to the Admin chat group. Maybe someone will recognize what is needed better than I. Feel free to join here, too! :slight_smile: You're invited to talk on Matrix

5

Hi Jennaj,

the problem is forwarded to our IT-people. I am running a galaxy-test-instance on a dedicated server, but now we are switching to a bigger resource where I do not have full admin rights and can not install additional tools like genemark or prothint. That will be their (IT) job :wink:

But many thanks for your help. I will run braker3 on my dedicated server from the command line. It’s not as convenient as doing it within galaxy but I do not need it so often.

Best regards

Felix

Mit freundlichen Grüßen

i.A. Dreyer Felix

1 Like
6

Hi! I think currently the best solution to run the braker3 tool is to use the Docker/Singularity official image, which includes an official license for genemark.
If you’re using TPV on your instance, you can do something like this: infrastructure-playbook/files/galaxy/tpv/tools.yml at 5ea1efa5390ebb259d300dc2c09f946377b407ac · usegalaxy-eu/infrastructure-playbook · GitHub

The tool was written to work in theory with conda package and manual install/license config, but in practice it’s too complicated to make it work like this.