bigWigToBedGraph: command not found - fatal error 127

Hi everyone,

I am trying to convert a BigWig file to a Bedgraph format by using local Galaxy. The tool that I added is called bigwig_to_bedgraph ( and it was installed according to the Galaxy tool tutorial ( No errors occurred during this process.

When I apply the tool to my BigWig file I get the following error: /Home/galaxy/database/jobs_directory/000/8/ line 9: bigWigToBedGraph: command not found.

I can’t figure out how to fix this problem although I am quite sure it is rather simple.

Any help is much appreciated.

Hi Stijn,

Did you download the dependencies to your instance from the admin page as well?


I also replied on your biostars post, but here some more detail.
Can you check your galaxy/config/galaxy.yml file, I think in your case if you use the following settings and restart galaxy it may be enough to get it working.

conda_auto_install: true
conda_auto_init: true

Hi Astrov,

The only dependency of this of bigWigToBedGraph is “package_ucsc_tools_312 revision 2d6bafd63401” and this was installed in the same way as mentioned in the tutorial (
Thank you for your interest in my topic.

Hi gbbio,

Thank you for your help. Unfortunately this did not work. I still receive the same error message: An error occurred while running the tool .

Execution resulted in the following messages:

Fatal error: Exit code 127 ()

Tool generated the following standard error:
/Users/Stijn/galaxy/database/jobs_directory/000/11/ line 9: bigWigToBedGraph: command not found

When I look in my directories, I can also only find everything up to /Users/Stijn/galaxy/database/jobs_directory/000. The 000 directory appears empty and the …11/ can’t be found anywhere. I am sorry if this is a ‘rookie’ question, I am really not familiar with the local galaxy environment.

No problem, it is expected that that folder is empty. It is just a temporary folder that is created automatically to store information about that specific job and will be removed when the job is done.

How did you installed package_ucsc_tools_312?

You could try to install the ucsc-bedgraphtobigwig @357 dependency. Go to the admin page and from there go to the “manage dependencies” page. From here you can install it.


Another tip that maybe could help you. If your start galaxy with the command sh --daemon it will automatically create a log file called galaxy.log in here you may find a better error. You stop galaxy again with the command sh --stop-daemon.

Alright thanks, that makes sense then. The package_ucsc_tools_312 was already installed when I first opened the local galaxy environment, but I also uninstalled and reinstalled it according to the Galaxy tool installer tutorial.

I also installed the ucsc-bedgraphtobigwig @357 dependency (but should it not be the other way around? ucsc-bigwigtobedgraph?):
Schermafbeelding 2020-07-28 om 16.44.30

Finally, I also used the sh --daemon command but the same issue remains.