Adds option to run FragPipe job with higher memory #770
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| @@ -71,6 +71,9 @@ | |||
| <!-- Only generate a workflow, don't run FragPipe --> | |||
| <param name="workflow_only" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Only generate the workflow output"/> | |||
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| <!-- Galaxy admins may utilize this variable to for jobs requiring higher memory --> | |||
| <param name="high_memory" type="boolean" checked="false" label="High memory job" help="This option is made available for Galaxy administrators to allocate more resources to FragPipe when selected. It may not be used by all systems - please contact your adminstrator to learn if your Galaxy instance does."/> | |||
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Sorry I missed some discussion I guess. How should a user know that? What is the use-case here?
Is the TPV rule not working?
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The TPV rule checks for this parameter. So this parameter will not be used by all installations, which I noted to the user in the help section.
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I'm not sure there's an exact precedent for this. I see that hifiasm also passes the parameter it uses for TPV to the program's command-line args, whereas this parameter is only used by TPV. But I thought this was a straightforward way to allow a user to request more memory, if the request can be fulfilled.
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I guess this can be cloned? |
Yes, thanks for the reminder. To document the discussion here - we are leaving the memory configuration choices to the admins alone, who can utilize input file sizes and other tool-related config. In the meantime, on usegalaxy.eu we simply increased the memory for all FragPipe jobs and it seems to be working well. |
The Galaxy administrator may use this variable to run the job with increased resources.