Utilize a high_memory Option in FragPipe Tool #1261
Conversation
reid-wagner
changed the title
files/galaxy/tpv/tools.yml
Outdated
| @@ -1444,3 +1444,10 @@ tools: | |||
| toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/.*: | |||
| cores: 8 | |||
| mem: 56 | |||
| rules: | |||
| - if: | | |||
There was a problem hiding this comment.
if think - id is missing, please look at the hifi example.
There was a problem hiding this comment.
I'm still getting AttributeError: 'Tool' object has no attribute 'params_from_strings' despite modeling hifiasm pretty closely. Any thoughts?
There was a problem hiding this comment.
@bgruening - I'm trying to dig into this further but I think I have hifiasm pretty well replicated, and I'm wondering if there's any piece I'm missing here?
There was a problem hiding this comment.
When I run tpv dry-run on the toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0, I get the same error. I don't know whether this rule was tested before or if something changed in the upstream codebase that handles the tool entity. I will have a further look and update you.
There was a problem hiding this comment.
I tried dry running with older versions, back to 2.1.0 and the error remained the same.
My Galaxy packages are all 22.1.1
There was a problem hiding this comment.
Thanks for looking into this @sanjaysrikakulam and @mira-miracoli!
That error is a known issue in the bioconda recipe and doesn't prevent the tool from running. We shouldn't need to set up the Java env either as the wrapper scripts do this already using the GALAXY_MEMORY_MB variable.
There was a problem hiding this comment.
The jobs fail as soon as they hit those errors. Maybe I am missing some parameters (I left everything to defaults)? Please test the tool and let us know if it works and we can proceed with this PR.
There was a problem hiding this comment.
Are these the automated tests as defined in the <tests> element that are running? These ran successfully in the most recent update here (galaxyproteomics/tools-galaxyp#769), and we do have successful jobs on the EU site as well.
There was a problem hiding this comment.
Nope. I started a job through the UI. For the data, I clicked on Generate Tour and did not change any parameters in the tool's UI. The jobs failed with the above error. If your jobs run in the EU without errors, we can proceed with this PR.
There was a problem hiding this comment.
I see. I'm not familiar with tours but we haven't built that for FragPipe.
reid-wagner
force-pushed
the
fragpipe_high_mem
branch
from
e4e36c8 to
144a85a
Compare
reid-wagner
force-pushed
the
fragpipe_high_mem
branch
from
144a85a to
80ed3d6
Compare
|
Thank you! |
|
We will deploy this tomorrow morning. |
While more typical FragPipe jobs are successful on GalaxyEU with the current settings, some larger searches are running out of memory. This would allow us to set a
high_memoryoption in FragPipe to increase allocated resources.