Brooke and colleagues:
On 12 Jul 2012, at 11:18, Brooke Rhead wrote: > Hi Chuck, > > At the moment, I'm seeing an error when I try to load the track hub: > > ERROR: Unsupported type 'bigWigd' in hub > > This appears to be a typo on the S7 trackDb definition . . . "type bigWigd" > should be "type bigWig". That might be responsible for S7 showing up in an > odd place. > > If fixing the typo doesn't fix the display problems, That did fix the S7 label position. Thanks Just in passing I would note (since I have spent a lot of time with tracks) that the utilization of real-estate in the left margin/legend is pretty inefficient. Control of significant digits and vertical labels would make them more legible and recover 5% of the pixels. > you can also take a look at the "visibility" and "priority" settings for > trackDb. We are working on documenting all of the settings relevant to track > hubs, and the work-in-progress is on our preview machine (keep in mind that > some of this could change): > > http://genome-preview.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html > > Visibility is described under "Common trackDb settings" and priority under > the "Common, though less frequently used settings" section. > Thanks I'll look there. > Regarding your questions: > > > 1. Would such a url be stable over long periods such that it can be > > included a published pdf? > > Yes, that is our intent. Track Hubs were developed to provide a stable way > for users to host and display their own data in the Genome Browser, without > any of the data being stored at UCSC, where it would be subject to our > expiration policies. If we change or add trackDb settings in the future, we > plan to continue to support settings for existing track hubs so that they > will continue to function as intended. So should there be a versioning tab for Track Hub to direct legacy support? > > > 2. Can you instruct me how to create such a url if for example I > > wanted to reduce the pixel with to 1400? > > You can set the pixel width by adding &pix=1400 to the url. If you leave the > setting out, pixel width is determined by a user's current pixel width > setting. If there is no such setting in a user's cart, it is determined by > the width of a user's web browser when the URL is clicked. > > Even though it is possible to set pixel width via the url, there is not > support for changing all browser settings in a track hub (akin to the > "browser" lines for custom tracks) yet. Adding a mechanism for changing > browser settings in track hubs is on our task list. OK. What is the "default"? It looks like it is 1405? It would make sense to have the initial display size be the one the Browser sets as default. Then support for user configuration starts at the same resolution? > > I hope this is helpful! If you have further questions, please contact us > again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group Thanks for the help. Cheers, Chuck _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
