xcms_xcmsset gives empty result about tools-metabolomics

[lecorguille]

Hi,
One which Galaxy instance did you use the xcms tools?

[bernt-matthias]

I installed it on our own instance (currently the dev branch).

[lecorguille]

Hum ... I have just tested using our Flavor:

docker run -d -p 8080:80 workflow4metabolomics/galaxy-workflow4metabolomics

And no problem for me

Did you use the Conda package or the tool_dependencies ?

[bernt-matthias]

The "Dependency Resolver Details" of 'xcms_xcmsset' list r-snow 0.4_1, bioconductor-xcms 1.46.0, and r-batch 1.1_4. All use Conda as Resolver.

[bernt-matthias]

How can I help to debug this further? I can see the command line in the logs and could try it directly. But I do not know which of the Rscript binaries that are found in my galaxy directory is used.

[lecorguille]

You can enable this option in your galaxy.ini:
cleanup_job = onsuccess

That way, you will be able to browse the working directory and launch the script named tool_script.sh(or something like that). It sets the Conda environment if there is one.

In the log, you can also check if it really manages to use the conda packages through a mulled environment or using aggregation of individual packages.

galaxy.tools.deps DEBUG 2017-08-28 09:52:04,481 Using dependency bowtie2 version 2.3.2 of type conda
galaxy.tools.deps DEBUG 2017-08-28 09:52:04,481 Using dependency samtools version 1.3.1 of type cond
galaxy.jobs.command_factory INFO 2017-08-28 09:52:04,535 Built script [/w/galaxy/galaxy3/database/job_working_directory/014/14148/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/w/conda/galaxy3/_conda/envs/mulled-v1-cf272fa72b0572012c68ee2cbf0c8f909a02f29be46918c2a23283da1d3d76b5" ] ||

[bernt-matthias]

Thanks a lot for the info.

The problem seemed to be a misconfiguration of our job runner.

Sorry for the inconvenience.

[lecorguille]

No problem
Thanks for your interest in our project :)