Question: External links to datasets, histories, workflows at Galaxy Main undergoing an update -- OPEN
gravatar for k.vanduijvenboden
3 months ago by
k.vanduijvenboden50 wrote:

Admin edit: Original title Galaxy hosted bigWig tracks disappeared in UCSC sessions


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,


links history galaxy share dataset • 219 views
ADD COMMENTlink modified 12 weeks ago • written 3 months ago by k.vanduijvenboden50

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

ADD REPLYlink written 3 months ago by k.vanduijvenboden50

Hi - There were some recent server configuration changes on UCSC's side that we adjusted to use at Galaxy Main 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

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k


Tests with bigwig display and saving into a UCSC Session do not reveal any problems when using

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:!forum/genome

Thanks! Jen, Galaxy team

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k

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.



ADD REPLYlink written 3 months ago by k.vanduijvenboden50


Hi Karel,

The broken link issue turns out to be a problem on the Galaxy Main side (specifically at 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!


ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 12 weeks ago by k.vanduijvenboden50

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

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


An issue ticket has been created to repair the share links. Please follow progress here:

Thanks again for reporting the issue (and for letting UCSC know the current status!).

Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour