SGPS works on galaxy EU but not on main.

Hi, I’m working trying to run SearchGUI & PeptideShaker on Galaxy main and I’m getting this error on PeptideShaker:

Archive: inflating: IdentificationParametersOutput.par An error occurred when saving the path preference to /usr/local/share/peptide-shaker-2.0.33-0/resources/conf/paths.txt. java.lang.RuntimeException:

This is my galaxy history: > > > > > Galaxy

It looks like the error message is due to saving the file and is an error within the tool.

I was working with Subina Mehta as well, one of the authors of the Proteogenomics tutorial. She confirmed that SGPS works on Galaxy EU, but is erroring on Galaxy main.

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Welcome, @Edwin_Huang

I’m reviewing. Thanks for reporting!

Hello again @Edwin_Huang

Yes, I can reproduce errors with certain settings but not with the default for SearchGUI. This is probably expected. Some options do not work well together and others seem to be picky. The tool form has explanations.

For Peptide Shaker, seems to always fail at ORG, and can get it to fail at EU with certain options.

For the GTN tutorials, only the Docker is technically supported. But if that is working at EU, then that is a bonus! Maybe the author can get the GTN updated to reflect the expanded “Available at these Galaxies” listing.

EU →

Hi @jennaj,

Thanks for the help! Does that mean I would have to run through the tutorial on the EU server, or is there any way for the tool on Galaxy main to be fixed?


Also, the error message on Galaxy main is different from the error message on Galaxy EU. Error on Galaxy main suggests that there is

error when saving the file to /usr/local/share/peptide-shaker-2.0.33-0/resources/conf/paths.txt,

while the error on Galaxy EU is:

Archive: inflating: IdentificationParametersOutput.par Path configuration completed. Fri Dec 01 21:46:18 CET 2023 Unzipping 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1.

Maybe there’s a bug with the script of Peptide Shaker on Galaxy Main causing that file save error? Can you get that fixed so Peptide shaker works on galaxy main?


Hi @Edwin_Huang

These are not fully supported yet on Maybe the developer you are discussing this with can help us to do that in the future. They can contact me here or at Github (same handle) if they need help. Or, can open a ticket if they notice what exactly is going wrong at this repository.

So, for now, work at the server where the tool seems to be available. Or, consider using the Docker. That said, if the developer is stating that it is ready to use at the server, that is good news. It also worked for me with the very tiny tool test data (that is what I shared).

If the tool errored for you at the EU server that could be for many reasons. Your error suggests that the tool ran out of resources reading in the input. Does the other log file have anything interesting in it? Or the expanded dataset? Are you sure the zip is intact? If it especially large – maybe try a smaller version to see what the compute limits currently are (these can sometimes be increased but not always… confirm the data is valid first and the parameters are appropriate). The tutorial data might be good to test with (larger than test data, plus scientifically representative). Find all logs/inputs/parameters in a summary on the job info page (“i” icon).

Update: if you want to send in a bug report for the error from the red dataset at ORG, we’d be interested in seeing it. It looks like a configuration problem.

Hi Jenna,

Sorry I wasn’t clear in my previous response. Both of the error messages were from your galaxy histories. When you ran peptide shaker using the same parameter configurations on EU and ORG, EU succeeded but ORG failed. When Peptide Shaker failed, they had different error messages shown in my previous reply.

When you say it’s a configuration problem, do you mean issues with the tool itself or when I configure the tool? Because from what I can tell from your Galaxy histories, for the same configuration, Peptide Shaker failed on ORG and succeeded on EU.

The person I’m working with developed the tutorial but not the tool. Who should I contact to have this issue fixed?

For now I’ll run on Galaxy EU.

Thanks for the help,

Hi @Edwin_Huang

For the configuration problem: that is something we need to work on at I was tracking this internally, but just created a public ticket you can follow for updates. Ticket → Fix configuration for Proteomics tutorial · Issue #667 · galaxyproject/usegalaxy-tools · GitHub

The changes will not be immediate, so yes, please run through the tutorial at the EU server or the Docker.