Update HTSJDK and picard versions

[bbimber]

No description provided.

[bbimber]

Hi @labkey-jeckels: this should be a pretty perfunctory update, but I cant create PR branches on server/platform anymore. This PR is currently targeting release25.3-SNAPSHOT; however, I think I need someone with write permissions to:

• Make a 25.3_fb_htsjdk on the labkey side of this fork
• Merge this single-line change into that branch (or maybe just edit the one line in github directly).
• Open a PR to merge that branch into release25.3-SNAPSHOT and let TeamCity run.

There is a related change here: BimberLab/DiscvrLabKeyModules#343

Would it be possible for someone at LabKey to help make that update? Thanks in advance for any help.

[labkey-jeckels]

I've created the mirror of the FB. TeamCity is running now.

[bbimber]

Thanks

[bbimber]

@labkey-jeckels: note, my second commit here (BimberLab/DiscvrLabKeyModules#343) should address that FastqRunner failure. I'm not sure if my commit on that PR will re-trigger team city though.

[bbimber]

I believe that JBrowse failure is a timing problem (i've never seen that particular issue before: https://teamcity.labkey.org/buildConfiguration/LabKey_253Release_External_Discvr_ExternalModulesTestPostgres/3602051), not related to this change.

Otherwise it seems to have passed.

[labkey-jeckels]

The JBrowse test passed on a rerun. The FastqRunner test failed on rerun, presumably because it's running against the LK fork of DiscvrLabKeyModules. Is the plan to merge your DiscvrLabKeyModules changes into the LK repo immediately afterwards?

[bbimber]

Team city doesn't pull from the same side of the fork?

Yes, I can do a merge to the LK side at the same time. This would be LabKey/DiscvrLabkeyModules on the release25.3-SNAPSHOT branch, right?

[bbimber]

@labkey-jeckels, this PR cherry picks the FastqcRunner / picard version changes on release25.3-SNAPSHOT: LabKey/DiscvrLabKeyModules#376

[labkey-jeckels]

Team city doesn't pull from the same side of the fork?

Yes, I can do a merge to the LK side at the same time. This would be LabKey/DiscvrLabkeyModules on the release25.3-SNAPSHOT branch, right?

This (and almost all other TeamCity builds) pull from the LabKey fork of the repo. The External/DISCVR projects pull from you copy of the repo.

Correct on the merge target.

[bbimber]

@labkey-jeckels: OK. What would you like prior to approving this PR? Do you want to restart the failed DRTs (it didnt look like I could re-trigger them myself). I believe that release25.3-SNAPSHOT targeting PR/branch will should be picked up by TeamCity now, right?

[labkey-jeckels]

@labkey-jeckels: OK. What would you like prior to approving this PR? Do you want to restart the failed DRTs (it didnt look like I could re-trigger them myself). I believe that release25.3-SNAPSHOT targeting PR/branch will should be picked up by TeamCity now, right?

I retriggered them manually and see your commits in the list of changes. Assuming it passes as expected I will go ahead and merge this PR.

[bbimber]

excellent, thank you