Hello,
I encountered this error while running Planemo test :
Job in error state.. tool_id: rrparser, exit_code: 127, stderr: /bin/bash: /tmp/tmp1_a2rwaf/job_working_directory/000/1/tool_script.sh: No such file or directory
.
what I can’t understand is that this tool “rrparser” has passed planemo test while updating the the wrapper with the new version of the conda package on an other PC. However, while running the same test with the same new version on my PC I get this error message. Thus I think that the error is more related to my PC but I couldn’t figure the reason. Moreover, this error appear not only for this tool, so it is not tool and wrapper dependent.
If any one had the same problem I would be happy if we can discuss about the way he could solve it.
Thank you.
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Hi @Ramiz.
I am also having the same issue as yours.
Unfortunately, I haven’t yet figured out what causes the problem.
Somehow the conda environment is not set properly.
I am using:
planemo 0.75.27
galaxy_sequence_utils 1.2.0
galaxy-tool-util 24.2.3
galaxy-util 24.2.3
galaxy2cwl 0.1.4
pulsar-galaxy-lib 0.15.7
Someone else had a problem that was resolved in a way that might be related. In short, the dependencies (and dependency order) the tools are using to execute might not be set up correctly. Galaxy needs to use a fresh version of miniconda that it will set up itself.
Other than that, this type of issue can be related to Python version problems in the full server implementation. We didn’t attract a developer yet since they might have confused this question with the other since they were so similar. We can ping them again.
can you give us the version of python, planemo, conda with their respective location please?
Also, you have to read with attention the logs in the Terminal and find the first error, which is maybe not the one you mentioned. I was stuck during two days by the error mentioned in my post mentioned by @jennaj and I found the solution by strutating very carefully logs in Terminal.
@Ramiz Are you using --biocontainers argument?
I only get the error when I use that. It is now fixed by completely removing Docker and Planemo, installing them again, and cloning a new galaxy.
Local Galaxy