bigWigToBedGraph: command not found - fatal error 127

[Stijn]

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 (https://toolshed.g2.bx.psu.edu/repository?repository_id=0dddb124b53a7bfd&changeset_revision=3799012ce2ff) and it was installed according to the Galaxy tool tutorial (https://galaxyproject.org/admin/tools/add-tool-from-toolshed-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/tool_script.sh: 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.

[astrov]

Hi Stijn,

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

[gbbio]

Hello,

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

[Stijn]

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 (https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/).
Thank you for your interest in my topic.

[Stijn]

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 toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0 .

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/tool_script.sh: line 9: bigWigToBedGraph: command not found

[Stijn]

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/tool_script.sh can’t be found anywhere. I am sorry if this is a ‘rookie’ question, I am really not familiar with the local galaxy environment.

[gbbio]

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.

EDIT:

Another tip that maybe could help you. If your start galaxy with the command sh run.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 run.sh --stop-daemon.

[Stijn]

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?):

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