Activity
From 09/09/2013 to 10/08/2013
10/08/2013
- 12:08 pm Feature #67 (Closed): change background color
- (suggested by Ting)
* Can user set background color? By default the background is white. Maybe someone wants it to...
10/07/2013
- 03:45 pm Bug #2 (Closed): chrome empty canvas
- * this issue has been solved with latest version of Google Chrome (Since Oct.2013)
- 11:13 am Bug #66 (Closed): Save custom metadata vocabulary into session
- Load a datahub containing a custom metadata, save it under session.
Either get "syntax error" on clicking Save but... - 09:44 am Bug #65 (Resolved): Error rendering RRBS track
- fixed in v24.2
- 09:26 am Bug #65 (Closed): Error rendering RRBS track
- http://epgg-test.wustl.edu/browser/?genome=hg19&hmtk=GSM621347
this shows a RRBS track. navigate to centromere reg... - 08:57 am Bug #44: long range track display weird in SVG output
- * seems still get abnormal output when open in inscape or illustrator
* please see screenshot below
- 07:29 am Bug #64 (Rejected): json hub not show custom meta colormap
- show:['Cell','Assay','Donor','View']
this line should be under "metadata", but not "vocabulary"
10/06/2013
- 09:58 pm Bug #64 (Rejected): json hub not show custom meta colormap
- * might I did it wrong way...
* in this hub: http://cgs.wustl.edu/~dli/remcMethyl.json
* I have show:['Cell','Assay... - 03:15 pm Bug #44 (Resolved): long range track display weird in SVG output
- 03:14 pm Bug #44: long range track display weird in SVG output
- SVG output function has been updated in v24.2, please see if this problem is still there. Also please do extensive te...
10/03/2013
- 09:22 am Revision 84c81131: preparing encode hub 2
- 09:22 am Browser Metadata Revision 84c81131: preparing encode hub 2
- 09:21 am Revision 4bbad921: preparing encode hub
- 09:21 am Browser Metadata Revision 4bbad921: preparing encode hub
10/01/2013
- 11:32 pm Bug #63 (Closed): Gene plot by Google Chart seems not working
- Google API now works. Closed.
- 01:52 pm Bug #63: Gene plot by Google Chart seems not working
- saw the trouble, because google API is not working:
https://www.google.com/jsapi 502 (Bad Gateway) - 01:23 pm Bug #63 (Closed): Gene plot by Google Chart seems not working
- * choose Google Chart for gene plot
* no figures comes out, and the interactive data table was not working either - 08:34 am Support #62 (New): "donor" terms in hg19 metadata
- There's lots of donor IDs in hg19 metadata, please make them more meaningful by adding sex/race/age/health informatio...
09/30/2013
- 09:59 pm Bug #61 (Closed): error embedding browser
- Fixed and closed
- 01:49 pm Bug #61 (Resolved): error embedding browser
- need to comply with the way metadata is declared in datahub: warp the metadata vocabulary inside the "vocabulary" key...
- 01:46 pm Bug #61 (Closed): error embedding browser
- error with embedding in v24.1
http://cgs.wustl.edu/~xzhou/plugin/2.html
09/28/2013
- 09:50 pm Bug #59: error filling contents for facet table of 2nd datahub
- works now
- 05:35 pm Feature #60 (Resolved): "file type" category for custom facet table
- Implemented in v24.1
A "File type" attribute is automatically added to metadata that's either loaded from hub or f... - 02:57 pm Bug #56 (In Progress): error handling with failed custom tracks
- better error handling implemented in v24.1. When a broken track is used, the browser should not crash but print out a...
- 08:20 am Feature #60 (Closed): "file type" category for custom facet table
- when a custom datahub or publichub is loaded, its inner metadata will be rendered into a facet table
it's also des... - 07:30 am Bug #59: error filling contents for facet table of 2nd datahub
- I first found and fixed this bug, then I posted here to log it
which one of the facet tables can't you click?
09/27/2013
- 11:28 pm Bug #59 (Feedback): error filling contents for facet table of 2nd datahub
- the Row and Column metadata header were not clickable
- 11:24 pm Bug #59: error filling contents for facet table of 2nd datahub
- went through your steps, no error found
- 11:23 pm Bug #57 (Closed): Can not import encode data. Just stop at importing...
- Closed. Might be re-opened if happened again.
- 04:11 pm Bug #59 (Resolved): error filling contents for facet table of 2nd datahub
- due to internal mdidx confusion, while loading a datahub
assumed that all coming datahub has mdidx of 1, actually sh... - 04:10 pm Bug #59 (Closed): error filling contents for facet table of 2nd datahub
- on hg19, load the GBM hub. in the "Tracks" panel, a facet table is shown for the GBM hub with tracks registered in it...
- 10:18 am Feature #58 (Closed): make publichubs for ENCODE tracks
- the "Dataset" feature will be retired
Instead the ENCODE tracks will be migrated into "publichub" format, which ma... - 09:52 am Bug #57 (Resolved): Can not import encode data. Just stop at importing...
- Fixed! Thanks,
- 09:47 am Bug #57 (Closed): Can not import encode data. Just stop at importing...
09/26/2013
- 01:50 pm Bug #56 (Closed): error handling with failed custom tracks
- in case of unacceptable custom track, don't crash or abort, but properly handle it and go on with it
- 09:27 am Bug #54: upload bigWig error
- * I think an error message like "your server doesn't support byte range request" would be more helpful
- 09:14 am Feature #55 (New): [System] killing subtleKnife process which had been stucked longer than 10min
- * did some research, finally choose to achieve this by using the killall command
* adding cron jobs to epgg1,2,3, au...
09/25/2013
- 01:28 pm Bug #54 (Rejected): upload bigWig error
- see what's wrong by running bwquery on this bigwig url
- 11:56 am Bug #54 (Rejected): upload bigWig error
- * submit a bigWig url as custom track will get an error
Uncaught TypeError: Cannot read property 'length' of undefin...
09/24/2013
- 07:25 am Bug #53 (Rejected): virus gene info display problem
- 07:25 am Bug #53: virus gene info display problem
- this is not an error
the graph is to indicate the structure of the whole gene
as the virus gene is just one exon, i...
09/23/2013
- 09:34 pm Bug #53: virus gene info display problem
- forget the screenshot..
- 09:33 pm Bug #53 (Rejected): virus gene info display problem
- * if you choose the virus genome, zoom in to base level
* click a gene, there is a blank area in the popup box
- 05:48 pm washugb v24 release
- We have applied version 24 browser today!
h1. New genomes
* Soybean _Glycine max_, version 189
* Common bean _...
09/22/2013
- 02:50 pm Feature #13: Line plot
- progress:
- matplot is now done using canvas
- can add tracks to a matplot, can remove tracks from one
- can show in ...
09/21/2013
- 07:14 pm Feature #52 (New): Improve gene set view
- (comments from Gormley, Matthew at UCSF)
* Would be nice to have a gene set view toolbar, including buttons for:
**... - 07:14 pm Feature #51 (New): Improve gene search function
- (comments from Gormley, Matthew at UCSF)
* Tracks -> keyword search "trophoblast" -> get too big of a list, select t... - 07:13 pm Feature #50 (New): Improve session?
- (comments from Gormley, Matthew at UCSF)
-saving a session is only useful if you remember to record the session ID. ... - 07:13 pm Feature #49 (New): general suggestions from UCSF
- (comments from Gormley, Matthew at UCSF)
*feedback window at upper right is too close to toolbar, relocate or remove...
09/19/2013
- 10:16 am Bug #46: Coordinate issue in hg19
- Now I see the problem. It is because on a wide zoom level in the browser, one pixel width of the horizontal axis span...
- 08:13 am Bug #46: Coordinate issue in hg19
- Weird.. I just tried on my laptop and still have the same problem but now the coordinate is different again..
- 07:45 am Bug #46: Coordinate issue in hg19
- cannot reproduce this problem
09/18/2013
- 10:59 pm Feature #48 (New): automatically refresh cache
- * I think it might be useful that the browser could refresh cache automatically
- 10:54 pm Bug #47 (Closed): wrong Y axis range display
- Solved and closed.
- 06:59 pm Bug #47 (Resolved): wrong Y axis range display
- Fixed. Please test it thanks!
- 06:26 pm Bug #47 (Closed): wrong Y axis range display
- showing hg18 mm1s default tracks
* applying rpm/bp normalization method to the read density data
* the five bam den... - 02:24 pm Bug #46 (New): Coordinate issue in hg19
- I found this issue in hg19:
Steps to reproduce:
copy chr5:131800537-131801093 into the coordinate window and cl... - 08:21 am Bug #43 (Closed): screenshot error on hub
- solved and closed!
- 08:18 am Bug #45 (Closed): mappability track display issue
- confirmed solved.
- 08:17 am Bug #45 (Resolved): mappability track display issue
- Fixed. This was a bug that under "automatic scale mode", if all values of the track are >0, the Y scale minimum value...
09/17/2013
- 11:00 pm Bug #45 (Closed): mappability track display issue
- * the browser display the 36mer mappability track with min value as 0
* a screenshot attached
* while if I query th... - 02:22 pm Bug #43 (Resolved): screenshot error on hub
- Thanks so much for finding this bug! The track that has trouble with SVG output is "grouped", which means it shares Y...
- 08:50 am Bug #31 (Closed): Cannot refresh Tabix index file
- 08:49 am Bug #44 (Closed): long range track display weird in SVG output
- * noticed this issue before, but could be solved by using PDF files instead
* currently a people mailed our list, he...
09/13/2013
- 10:08 pm Bug #37 (Closed): track loading indicator text always display 'working' after finish of loading
- closed!
- 09:58 pm Bug #38 (Closed): new hub Turn off Gene Set View not work
- closed!
- 09:58 pm Bug #39 (Closed): json syntax error when running gene set view
- closed!
- 09:58 pm Bug #40 (Closed): gene plot crashed on gene set of json hub
- 09:57 pm Bug #41 (Closed): scatter plot json error
- 09:57 pm Bug #40: gene plot crashed on gene set of json hub
- closed!
- 09:57 pm Bug #41: scatter plot json error
- closed!
- 09:57 pm Bug #42 (Closed): json hub load error
- closed!
- 09:56 pm Bug #43 (Closed): screenshot error on hub
- * using hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* Apps->Screenshot
* An error 'Uncaught TypeError: Can... - 12:19 pm Bug #37 (Resolved): track loading indicator text always display 'working' after finish of loading
- fixed in v23.3, please test, thanks!
- 09:07 am Feature #14 (Closed): Custom categorical track
- 09:06 am Feature #34 (Closed): add soybean genome
- 09:06 am Feature #35 (Closed): add common bean genome
- 09:06 am Feature #36 (Closed): add Brassica Rapa genome
- 07:33 am Bug #42 (Resolved): json hub load error
- fixed
Change to datahub json format: json objects must be enclosed inside [] (on test browser)
09/12/2013
- 10:24 pm Bug #42 (Closed): json hub load error
- * use the hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* missing type information error
* repeat 3 times - 08:34 am Bug #41 (Resolved): scatter plot json error
- fixed on test browser
- 08:34 am Bug #40 (Resolved): gene plot crashed on gene set of json hub
- fixed on test browser
- 08:34 am Bug #39 (Resolved): json syntax error when running gene set view
- fixed on test browser
- 08:33 am Bug #38 (Resolved): new hub Turn off Gene Set View not work
- fixed on test server
09/11/2013
- 09:43 pm Bug #41 (Closed): scatter plot json error
- * using json hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* select scatter plot for 1st gene set with any 2 ... - 09:42 pm Bug #40 (Closed): gene plot crashed on gene set of json hub
- * using hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json for hg19
* do gene plot on 2nd gene set
* crashed with... - 09:41 pm Bug #39 (Closed): json syntax error when running gene set view
- * using the hub for hg19: http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* run gene set view on 2nd gene set
* cr... - 09:39 pm Bug #38 (Closed): new hub Turn off Gene Set View not work
- * using the new json hub for hg19: http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* after gene set view on 1st gen...
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