Activity

From 07/22/2013 to 08/20/2013

08/20/2013

10:57 pm Feature #33 (New): batch GEO id output
* I was thinking a function like output all the GEO id of the tracks currently displayed
* It might be useful for us...
Daofeng Li

08/07/2013

09:32 am Bug #32 (Closed): right click twice caused background color change
closed due to not a real bug. Daofeng Li
09:21 am Bug #32: right click twice caused background color change
* I agree with you, it should be related to web browsers.
* anyway, I tested again at Mac, only reproduce it at Chro...
Daofeng Li
07:13 am Bug #32: right click twice caused background color change
I can't reproduce it, it should be a issue with web browser, not the genome browser Xin Zhou

08/06/2013

11:24 pm Bug #32 (Closed): right click twice caused background color change
* might be not a bug while it just happened on my computer
* I am using Google Chrome in Windows 7
* open browser, ...
Daofeng Li
07:25 pm Bug #31 (Resolved): Cannot refresh Tabix index file
failed to properly reconstruct path of cached tabix index file
suppose a track is http://domain.com/path/to/file.g...
Xin Zhou
07:22 pm Bug #31 (Closed): Cannot refresh Tabix index file
Cannot refresh Tabix index file Xin Zhou
02:59 pm washugb v23 release
We have applied version 23 of washugb code to our public servers today.
h2. Updates:
## custom categorical trac...
Daofeng Li
01:28 pm Browser Metadata Revision 71d28e6f: update with v23
Daofeng Li
01:28 pm Revision 71d28e6f: update with v23
Daofeng Li

08/05/2013

04:50 pm Feature #30 (New): bam track (full) view range limit
* in UCSC browser, when you zoom out like 1/4 chromosome range, the repeatmasker tracks will show 'zoom in to <= 10,0... Daofeng Li

08/04/2013

09:39 pm Bug #29 (Closed): make url didn't save secondary panel
solved Daofeng Li

08/03/2013

11:46 pm Bug #29 (Closed): make url didn't save secondary panel
* just open a secondary panel
* choose make url, click the url navigate to a new window, the secondary panel was not...
Daofeng Li
11:43 pm Feature #28 (New): add time information for session and status
* just think it might be useful to add time information to the session and status in saved session Daofeng Li
11:38 pm Bug #27 (Closed): retrieve session with custom categorical track error
Daofeng Li
11:37 pm Bug #24 (Closed): rule display problem when open secondary panel
Daofeng Li
11:37 pm Bug #24: rule display problem when open secondary panel
solved and closed. Daofeng Li
11:36 pm Bug #27: retrieve session with custom categorical track error
confirmed solved and closed. Daofeng Li
02:53 pm Bug #27: retrieve session with custom categorical track error
I am still getting same error on hg18.
Your session above works.
the session: XivUTiiNel was I just created.
I als...
Daofeng Li
01:40 pm Bug #27 (Resolved): retrieve session with custom categorical track error
code has been changed and your trial session has gone invalid
try this one on hg18: yT9pbEppjc
Xin Zhou
12:59 pm Bug #27 (Closed): retrieve session with custom categorical track error
* steps to reproduce:
## open hg18 default tracks
## add the example custom categorical track
## save session
#...
Daofeng Li

08/02/2013

10:17 am Bug #26 (Closed): categorical track submit json error
confirmed solved.
Also the hub works now.
Daofeng Li
08:56 am Bug #26 (Resolved): categorical track submit json error
Xin Zhou
08:53 am Bug #26 (Closed): categorical track submit json error
* use the example url for hg18 and hg19 respectively
## hg18: http://epgg-test.wustl.edu/cc.gz
## hg19: http://vi...
Daofeng Li
07:50 am Feature #14 (Resolved): Custom categorical track
Xin Zhou
07:49 am Feature #25: Quick capture of the central canvas
very nice attempt! Xin Zhou

08/01/2013

11:54 pm Feature #25 (New): Quick capture of the central canvas
* I have tried developing a plugin for quick capture the central canvas as a PNG figure
* enable this plugin is easy...
Daofeng Li

07/30/2013

02:14 pm Feature #14: Custom categorical track
Do you mind put this issue to a higher priority? Thanks. Daofeng Li

07/29/2013

09:49 pm Bug #24 (Closed): rule display problem when open secondary panel
* little display problem
* adjust the rule to screen wide
* open secondary panel, you will found the rule still acr...
Daofeng Li
12:15 pm Bug #18 (Closed): embed example 2 from test not working
Daofeng Li
12:14 pm Feature #19 (Closed): new url parameter for public hub
Daofeng Li
12:14 pm Bug #12 (Closed): message after datahub submission confusion
Daofeng Li
12:13 pm Bug #20 (Closed): track information display problem
Daofeng Li
12:13 pm Bug #22 (Closed): no thing happens when click information after right click on refgene track
Daofeng Li
12:13 pm Bug #23 (Closed): metadata colormap not added for public hub by url parameter
Daofeng Li

07/28/2013

12:24 pm washugb v22 release
We have applied v22 source code to our public servers.
h2. updates:
Please see our blog plots for details:
#...
Daofeng Li
07:10 am Bug #23 (Resolved): metadata colormap not added for public hub by url parameter
Use "metadata" parameter in URL to add terms to colormap. Xin Zhou

07/27/2013

04:48 pm Bug #23 (Closed): metadata colormap not added for public hub by url parameter
* if access the public hub by url parameter, will found the meta colormap was not added Daofeng Li
03:52 pm Feature #19 (Resolved): new url parameter for public hub
Thanks for the suggestion! See this example: http://epgg-test.wustl.edu/browser/?genome=hg18&publichub=mm1s Xin Zhou
03:38 pm Bug #22 (Resolved): no thing happens when click information after right click on refgene track
Xin Zhou
03:38 pm Bug #20 (Resolved): track information display problem
Xin Zhou
03:37 pm Bug #12 (Resolved): message after datahub submission confusion
Xin Zhou

07/26/2013

10:25 pm Bug #22 (Closed): no thing happens when click information after right click on refgene track
* just right click on refgene track, selection information, nothing happened
* see screenshot
Daofeng Li
02:47 pm Feature #21 (New): operation history
* Is it possible or useful to add the history of operations for the browser (back to some operation steps before etc)... Daofeng Li
11:18 am Bug #20 (Closed): track information display problem
* see the attached picture, the url displayed out of the box Daofeng Li
11:02 am Bug #18: embed example 2 from test not working
* confirmed solved.
* since the code will continue update, and this issue might happen again, we could left it as op...
Daofeng Li
10:55 am Feature #19 (Closed): new url parameter for public hub
* I am thinking a url parameter for public hub would be useful for loading hub by single click
* example like pubhub...
Daofeng Li
10:52 am Bug #18 (Resolved): embed example 2 from test not working
Xin Zhou
10:47 am Feature #7 (Closed): store gene set info in datahub descriptor file
Xin Zhou
10:44 am Bug #18 (Closed): embed example 2 from test not working
* visiting url: http://cgs.wustl.edu/~xzhou/plugin/2.html
* an error happens: Uncaught ReferenceError: trackstyle_co...
Daofeng Li

07/25/2013

09:42 pm Feature #17 (New): public datahub unload button?
* I noticed that after I loaded a json datahub, the 'remove all' cannot be used to remove all added tracks (not a bug... Daofeng Li
07:08 pm Revision 5f46a05f: hg18 public hub added
Daofeng Li
07:08 pm Browser Metadata Revision 5f46a05f: hg18 public hub added
Daofeng Li
07:07 pm Revision ed2c5f6e: public hub added
Daofeng Li
07:07 pm Browser Metadata Revision ed2c5f6e: public hub added
Daofeng Li

07/24/2013

04:51 pm Revision 8c368a17: first init
Daofeng Li
04:51 pm Browser Metadata Revision 8c368a17: first init
Daofeng Li

07/23/2013

01:44 pm Feature #1 (Rejected): switch genome button
Xin Zhou
08:00 am Feature #14 (Closed): Custom categorical track
the browser still lacks custom track support for categorical tracks Xin Zhou
07:59 am Feature #13 (New): Line plot
Line plot is the new rendering mode for numerical tracks. Multiple tracks can be rendered in the same canvas sharing ... Xin Zhou

07/22/2013

05:45 pm Bug #12 (Closed): message after datahub submission confusion
* I was trying to submit a hub with 3 bam files, all display type were set to hide
* when I submit the hub, I was to...
Daofeng Li
05:40 pm Feature #11 (New): ability to cancel a super-enhancer job
* I just click 'submit' too quickly without specify an input bam, would it be good to add this option to allow cancel... Daofeng Li
05:35 pm Feature #10 (New): gene set list in hub support url
Is it possible that to enable url support in the new gene set list in datahub descriptor file?
For genes, the file...
Daofeng Li
02:09 pm Browser Metadata Bug #4 (Closed): danRer7 assay H2AFV_ChIP-chip misplaced
Xin Zhou
02:09 pm Bug #8 (Closed): Datahub submission Json error
Xin Zhou
02:09 pm Bug #6 (Closed): scatter plot shared between genomes and caused Json syntax error
Xin Zhou
02:08 pm Bug #9 (Closed): no necessary 'Go Back' button after datahub submission
Xin Zhou
01:40 pm Bug #9 (Closed): no necessary 'Go Back' button after datahub submission
*The 'Go Back' button should not appear after datahub submission
* if uses click it, the button will just disappear
Daofeng Li
11:07 am Bug #8: Datahub submission Json error
I missed a step in updating/installing browser code:
update tabix library by compiling original source code
tha...
Xin Zhou
11:00 am Bug #8 (Resolved): Datahub submission Json error
Xin Zhou
10:56 am Bug #8 (Closed): Datahub submission Json error
Trying to batch upload tracks. Worked last week before the latest update.
Datahub file: http://remc.wustl.edu/jgu...
Junchen Gu
10:18 am washugb v21 release
We just applied the v21 source code to our public servers.
h2. Function updates:
## the new 'Gene Set' under '...
Daofeng Li
10:14 am Feature #7 (Closed): store gene set info in datahub descriptor file
user can put gene sets or regions in hub descriptor file, so that this information is persistent and won't be lost wh... Xin Zhou
09:33 am Bug #6 (Resolved): scatter plot shared between genomes and caused Json syntax error
Xin Zhou
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