Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • Sep 29 19:42
    joshsadam synchronize #1280
  • Sep 29 18:01
    ksierks synchronize #1362
  • Sep 29 13:19
    joshsadam synchronize #1280
  • Sep 29 12:54
    joshsadam synchronize #1280
  • Sep 29 10:48
    joshsadam synchronize #1280
  • Sep 29 10:41
    joshsadam synchronize #1280
  • Sep 29 04:37
    joshsadam synchronize #1280
  • Sep 29 03:50
    joshsadam synchronize #1280
  • Sep 29 03:29
    joshsadam synchronize #1280
  • Sep 29 03:12
    joshsadam synchronize #1280
  • Sep 29 02:18
    deepsidhu85 edited #1370
  • Sep 29 02:18
    deepsidhu85 edited #1370
  • Sep 29 01:54
    deepsidhu85 ready_for_review #1374
  • Sep 29 01:54
    deepsidhu85 synchronize #1374
  • Sep 29 01:53
    joshsadam synchronize #1370
  • Sep 29 01:53
    joshsadam closed #1366
  • Sep 29 01:23
    deepsidhu85 synchronize #1374
  • Sep 29 00:13
    deepsidhu85 synchronize #1374
  • Sep 29 00:01
    deepsidhu85 labeled #1374
  • Sep 29 00:01
    deepsidhu85 labeled #1374
Karin Lagesen
@karinlag
apologies if this is a faq somewhere, but is there an api to get metadata into the system, and to get results out of it?
Aaron Petkau
@apetkau
@karinlag there should be an HTTP GET command for getting metadata from a project: https://phac-nml.github.io/irida-documentation/swagger-ui/index.html#/projects/getProjectSampleMetadata
There are some POST and PUT commands in there too for putting metadata into the system
Though I don't know exactly how complete they are right now for e.g., batch upload of metadata to an entire project
Though we do that periodically, so I'd have to check how it's done currently (there has been discussion on how to make this more efficient for all the SARS-CoV-2 genomes we have)
Karin Lagesen
@karinlag
thanks, @apetkau !
Aaron Petkau
@apetkau
:smile:
Jeffrey Thiessen
@JeffreyThiessen
@karinlag Here is some code we have been using metadata uploads using the python api for irida from the irida uploader codebase. https://github.com/phac-nml/ncov2019-artic-nf/blob/update/sample_naming/bin/upload.py
You'll probably have to modify it heavily to fit your use case but it should give you a good idea of the code flow
Karin Lagesen
@karinlag
thanks so much @JeffreyThiessen !
this is exactly what we need :)
Eric Enns
@ericenns
Hi everyone. Thanks to @apetkau we created a 21.09.2 release to fix some old dependencies that had Critical|High issues as reported by Grype. Note the only one which would have been the easiest to exploit was excel parsing used by the metadata importer. (https://github.com/phac-nml/irida/releases/tag/21.09.2)
More information can be found here (https://github.com/phac-nml/irida/blob/master/UPGRADING.md).
Aaron Petkau
@apetkau
Thanks @ericenns . The specific changes we made are in the PR: phac-nml/irida#1149
George Marselis @NVI
@georgemarselis-nvi
I miss IRC...
hi guys
George Marselis @NVI
@georgemarselis-nvi
irida latest 21.0.1 i think: war deploys, page reports 404 when navigated to
this is on tomcat 10
George Marselis @NVI
@georgemarselis-nvi
i know the app is configured right, cuz i made a copy of the original app started right away
anyways, happy holidies get back to me when you can
pvanheus
@pvanheus
@georgemarselis-nvi can you past the log somewhere? and how did you start up the IRIDA server?
George Marselis @NVI
@georgemarselis-nvi
@pvanheus sure, but the log is squeaky clean
@pvanheus the irida server? you mean tomcat?
George Marselis @NVI
@georgemarselis-nvi
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.
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:
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.