Repeat masker and Locarna issues


#1

Hi again,

I’m trying to run Repeat Masker (Galaxy Version 4.0.7+galaxy1) in my local Galaxy (v18.09). I uploaded the repbase file and a fasta file to searching for the repeats. The job doesn’r run and return this:

Fatal error: Exit code 1 ()
dirname: falta operando
Try ‘dirname --help’ for more information.

With Locarna I receive only: Unable to finish job.

I would appreciate any help.
Thanks!
Rubens.


#2

Hi there Rubens

I suspect that this could be caused by RepeatMasker not being present in the environment where this tool this running. I have just submitted a pull request to do better testing, but the current version of the tools-iuc RepeatMasker wrapper simply assumes that RepeatMasker will be in the PATH.

Can you please check with your Galaxy Administrator that the RepeatMasker dependency has been installed correctly?

Peter


#3

That’s a problem. I’m the admin. I install RepeatMasker with the toolshed. It seems that all dependencies are installed, nothing is wrong. Should I try reinstall?

What about Locarna problem? That actually have dependencies that I couldn’t install. Maybe this is the problem.

Thanks


#4

I don’t know about the Locarna problem. Is that the one from rnateam?

I recommend that you try and reinstall the tool depencies for RepeatMasker, at least until the PR I am working on is merged.


#5

I’ve updated the RepeatMasker wrapper - please update on your side and see if the feedback is more meaningful.


#6

Hi,
Now I have this message: Fatal error: Exit code 1 ()

I installed the full version, and everything was fine, including dependencies, and I’m trying to use the commands, by so far it says that the command doesn’t exists. For sure I’m doing something wrong…


#7

@rubens can you try locarna at usegalaxy.eu and report the problem to me. We a very good relationship to the locarna dev, so my hope is to get him to look at it in more detail.