search

rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
58 stars 17 forks source link

Updated Docker image #70

Closed akogler closed 11 months ago

akogler commented 1 year ago

Hi Rick,

Is the latest Docker image updated to patRoon v 2.2? I am running patRoon using this modified singularity file. It has been working without issue until I recently started testing out the sets workflow and ran into the following error during the componentization step:

Error in .local(fGroups, components, prefAdduct, ...) : No adduct/isotope information available in given components! Calls: selectIons ... Map -> mapply -> -> -> .local Execution halted

This happens when I try to run this command: fGroupsSel <- selectIons(fGroups, componOpenMS, c("[M+H]+", "[M-H]-"))

Based on what I read about changes from patroon v 2.1 to 2.2, it seems like this error may have been fixed and I'm wondering if that update isn't reflected in the Docker image yet because I am pulling the latest Docker image each time. Thank you!

rickhelmus commented 1 year ago

Hello,

Thanks for your report. CI was stuck and needed some attention, but a new Docker image should be available now. Hopefully this fixes the problem!

akogler commented 1 year ago

Hi Rick,

Thanks for looking into the issue! I see that the Docker image was updated just yesterday but I think it might still be version 2.1 if I am looking in the correct spot on Docker Hub (line 19). dockerHub

When I run patRoon, it indicates that version 2.1.0 is being used. Could you double check if there might still be an issue with the Docker image? Thanks so much!

rickhelmus commented 1 year ago

Hello,

I just pulled the latest image and it seems up to date. Note that the version you mention is not from patRoon, but from the S6 init system used by the rocker base image.

Are you still observing the issue with selectIons()?

akogler commented 1 year ago

Hi Rick, I am still experiencing the same issue with selectIons(). slurm-14992932.txt is the output file that is generated when I try to run the componentization step during a sets workflow. This is the R script that I am trying to run.

When patRoon is initialized in R, the message "Welcome to patRoon 2.1.0" appears. I thought that the latest version of patRoon should be pulled from Docker Hub each time I run a job that uses the singularity file I linked in my first comment. It seems that this isn't actually working. Given that the Docker images moved to a new host, I'm wondering if I need to modify my singularity file?

Based on the code and output I shared above, do you think there might be something causing the error other than the version issue?

Thanks, Anna

rickhelmus commented 1 year ago

Hi Anna,

You are right that the welcome message hints on an older version of patRoon. Unfortunately, I have zero experience with singularity, so I cannot be much of a help with that, sorry... But it seems reasonable to first figure out how to ensure that singularity pulls the latest Docker image, then we can see what to do if you are still facing the issue with componentization.

Thanks, Rick

rickhelmus commented 11 months ago

Closed due to inactivity, feel free to re-open!