Question: External links to datasets, histories, workflows at Galaxy Main https://usegalaxy.org undergoing an update -- OPEN
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k.vanduijvenboden • 50 wrote:
Admin edit: Original title Galaxy hosted bigWig tracks disappeared in UCSC sessions
Hello,
I have a number of tracks that I processed to bigWigs on Galaxy and imported to UCSC browser sessions. The bigWig tracks remained hosted on Galaxy, but always loaded again into (saved) UCSC sessions automatically.
Since last weeks all Galaxy hosted tracks have disappeared in all my UCSC sessions (whereas they have been stable for years). Idem for my co-workers. Any idea what causes this issue and if it can be fixed? Of course it's possible the problem is on the end of UCSC, so I will send them an email too.
Best regards,
Karel
Hi Jennifer,
Thanks for looking into this (!) and I hope the problem can be resolved. I sent a mail to UCSC support to update them with the new info you just posted here in this topic.
Cheers, Karel
Hi - There were some recent server configuration changes on UCSC's side that we adjusted to use at Galaxy Main https://usegalaxy.org. This hasn't been reported as a problem. I am running a functionality test and asking the developers for feedback. More soon, thanks! Jen, Galaxy team
Hello,
Tests with bigwig display and saving into a UCSC Session do not reveal any problems when using https://usegalaxy.org.
Are your missing bigwig datasets still marked as active (not deleted or purged) in Galaxy? Please double check -- they must be active to be persistently available to external applications.
If active and still not reliably loading, then yes, this could be a UCSC issue, especially given that the data are missing sometimes and other times not when loading a Session. Or it may be that sometimes you are actually saving changes versus bringing up what is already cached (and temporary). I've always needed to actively decide to "save" new Sessions and/or tracks added to existing Sessions using their website/forms. And, as far as I know, any Session change no matter how minor (content, descriptions, sharing) requires a save to be persistent. Once logged out, anything not specifically saved becomes a lost change.
You'll need to ask them about this if that doesn't seem to be your case (unsaved Session modifications) ... perhaps functionality has changed? This is their Google support forum if you need more help/clarification from them: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome
Thanks! Jen, Galaxy team
Hello Jennifer,
Thanks for your answers. I confirm that the bigWigs are still active and the changes in UCSC sessions were long ago made persistent through saves. Adding 'new' bigWigs to UCSC sessions indeed works fine. It's just that my older sessions have lost them. You are probably right that this is something on the end of UCSC, I will report this on their google support forum.
Thanks!
Karel
Update:
Hi Karel,
The broken link issue turns out to be a problem on the Galaxy Main side (specifically at https://usegalaxy.org). This is due to a different server upgrade than I had considered originally and impacts all pre-existing external links to datasets, plus a few other items.
UCSC cannot resolve the problem -- so if you already asked them a question, please send them an update and link back here.
We are working on a correction right now and will update/close out this post once resolved. There isn't a tracking ticket yet but if one is needed (this persists for longer than a day more), we'll create link one back for progress status, too.
Thanks for reporting the problem and checking your session content - not saving changes is usually the root of the problem when that type of issue comes up, but not this time!
Jen
Hello Jennifer, Galaxy team,
I hope I'm not too impatient with this message, but the shared Galaxy tracks have not reappeared in our UCSC sessions yet. Please let me know if this will take longer to resolve, then I will need to invest some time in replicating UCSC sessions for co-workers in my department (not to mention my own sessions) :)
Thanks! Karel
Hi - The change to create persistent links for datasets is still a work in progress and it is unclear still how older non-persistent links will be handled.
For now, link the datasets in again to UCSC (or wherever else they are included) using the current link given to the dataset in Galaxy (link copied from the "disc" icon, per dataset).
Thanks! Jen