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George Marselis @NVI
@georgemarselis-nvi
@pvanheus the irida server? you mean tomcat?
https://gist.github.com/georgemarselis-nvi/928b7d69780ceb626afd94bc20afbd80 here is the tomcat systemd service
George Marselis @NVI
@georgemarselis-nvi
you can grab the logs from here https://www.dropbox.com/s/4f318ql3zn2dxv7/logs.tar.gz?dl=0
https://www.dropbox.com/s/4f318ql3zn2dxv7/logs.tar.gz
https://www.dropbox.com/s/4f318ql3zn2dxv7/logs.tar.gz?dl=1
last link is better cuz it autodownloads
middle link will open the remote file in the dropbox site
Eric Enns
@ericenns
@georgemarselis-nvi Java 11 or higher is required for IRIDA and from looking at your logs specifically line 35353 in catalina.out it shows that java 8 is being used.
Java 11 requirement noted here https://phac-nml.github.io/irida-documentation/administrator/web/
pvanheus
@pvanheus
and btw Tomcat must be version below 10
(they change a bunch of interfaces in 10)
George Marselis @NVI
@georgemarselis-nvi
hmmm
ok, i'll try again
thank you and sorry to bother you during holidays
Karin Lagesen
@karinlag
Happy New year folks
Out of curiosity, I am wondering what frameworks and other things that are used to create Irida
I have seen some references to Spring I think?
Anything else that would be useful to know when looking into things?
Aaron Petkau
@apetkau
Happy New Year :smile: :fireworks:
There is a small list right here https://phac-nml.github.io/irida-documentation/developer/getting-started/#languages-and-libraries
But there's likely more than that
Spring is a big one though
Karin Lagesen
@karinlag
thanks @apetkau
that gives me something to go on :)
Jeevan Karloss
@ajkarloss

Good morning.

We are installing the tools for thee default (Assembly, Annotation, Mentalist, SISTR....) pipelines using shed-tools command mentioned in the documentation page (https://phac-nml.github.io/irida-documentation/administrator/galaxy/existing-galaxy/)

It got timed out while installing and the tools are not installed properly.

Is there a way to delete them and install them from start? When we execute the shed-tools command again, it says the tools are installed already

But they are not
@pvanheus any tips here?
pvanheus
@pvanheus
@ajkarloss this is one of the reasons why I switched to using Singularity for tools. I had to go through multiple steps of manual uninstalling and reinstalling to get everything working.
one workaround though to make conda less painful is to install mamba in the Galaxy conda environment, and set conda_exec in the Galaxy config to point to the mamba executable (i.e. conda_exec: /tool_deps/_conda/bin/mamba in our config)
Jeevan Karloss
@ajkarloss
Ok. I am deleting them from the browser and reinstalling them now
@pvanheus Thanks
Aaron Petkau
@apetkau
Thanks for the advice @pvanheus
If a tool fails to install I tend to delete and re-install from the Galaxy UI: https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/. But that's maybe not ideal if there are many tools with issues.
pvanheus
@pvanheus
@apetkau its really a Galaxy fault if things don't install right, but unfortunately I see it happening too often - especially with complex tools with lots of (conda) dependencies.
Karin Lagesen
@karinlag
are there ways to do this from the commandline?
(says the person who is more than slightly naive on this front)
pvanheus
@pvanheus
to delete and re-install? not that I have found...
Karin Lagesen
@karinlag
:(
pvanheus
@pvanheus
btw I don't know if I see this problem more often because I have a particularly slow Galaxy server (I think it might be slow because the filesystem isn't great at handling metadata operations and conda does a lot of those)
Karin Lagesen
@karinlag
hmmm.... @ajkarloss didn't our other companion say something about our filesystem being slow?
could this be a potential source of this annoyance?
pvanheus
@pvanheus
this is something that perhaps should be raised in the Galaxy admins world / on their Gitter channel. of course, quantifying the problem first would be helpeful :)
Karin Lagesen
@karinlag
(thumbsup)
pvanheus
@pvanheus
hello IRIDA folks .... can this PR please be included in IRIDA 22.01? phac-nml/irida#1140
9 replies
Jeffrey Thiessen
@JeffreyThiessen
Irida Uploader version 0.7.1 is released. It contains a bugfix for the intermittent 10054 connection errors that some network-controllers/firewalls give when uploading data. Hopefully this problem is fixed for good now. https://github.com/phac-nml/irida-uploader/releases/tag/0.7.1 https://anaconda.org/bioconda/irida-uploader
Jeevan Karloss
@ajkarloss

Getting this error while submitting a pipeline. Where the problem could be? Is it in the communication between IRIDA and Galaxy or permission issues?

11 Jan 2022 09:26:30,737 DEBUG ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl:117 - Preparing AnalysisSubmission [id=11, name=SISTR1-11-2022_Test_1, submitter=admin, workflowId=b21ea62c-7916-4ca6-96ba-90c20177b70f, analysisState=NEW, analysisCleanedState=NOT_CLEANED]
11 Jan 2022 09:26:30,853 DEBUG ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync:105 - Preparing submission for AnalysisSubmission [id=11, name=SISTR1-11-2022_Test_1, submitter=admin, workflowId=b21ea62c-7916-4ca6-96ba-90c20177b70f, analysisState=PREPARING, analysisCleanedState=NOT_CLEANED]
11 Jan 2022 09:26:30,868 ERROR ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect:65 - Error occured for submission: AnalysisSubmission [id=11, name=SISTR__1-11-2022_Test_1, submitter=admin, workflowId=b21ea62c-7916-4ca6-96ba-90c20177b70f, analysisState=PREPARING, analysisCleanedState=NOT_CLEANED] changing to state ERROR
ca.corefacility.bioinformatics.irida.exceptions.galaxy.WorkflowUploadException: Could not upload workflow from /workflows/1.1.1/irida_workflow_structure.ga
at ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService.uploadGalaxyWorkflow(GalaxyWorkflowService.java:64) ~[classes/:?]

Jeevan Karloss
@ajkarloss
@everyone, Do anyone have IRIDA plugin .jar file for latest (0.2.4 or 0.2.5) Mentalist?
The .jar file available for is 0.1.9 from 2018
Jeevan Karloss
@ajkarloss
One more stuff: We have deleted some fastq files from our IRIDA installation. But the project and sample names are still there in IRIDA weeb. Since the data is not deleted physically from disk (by IRIDA), is there an easy way to re-associate the data to the project and sample instead of re-uploading?
Aaron Petkau
@apetkau
For the error with SISTR, can you try directly uploading the workflow into Galaxy (https://github.com/phac-nml/irida-plugin-sistr/blob/master/src/main/resources/workflows/1.1.1/irida_workflow_structure.ga )? I assume that Galaxy is still missing some tools.