Activity

From 02/07/2014 to 03/08/2014

03/08/2014

11:13 am Bug #175: alignment issue with 2nd panel
duplicating with #86, please keep track of things Xin Zhou

03/07/2014

07:26 am Bug #176 (Rejected): browser is not drag-move when there is no track in central canvas
Xin Zhou

03/06/2014

11:31 pm Bug #176 (Rejected): browser is not drag-move when there is no track in central canvas
* think about this situation
* I fired up the browser, added one long range track, when I want to drag and move, I c...
Daofeng Li
11:29 pm Bug #175: alignment issue with 2nd panel
* forget the figure.. Daofeng Li
11:28 pm Bug #175 (Closed): alignment issue with 2nd panel
* please see attachment figure for alignment issue
* there are additional space below meta header, and above rmsk_en...
Daofeng Li
11:27 pm Bug #174 (Closed): 2nd panel background color issue
Daofeng Li
05:23 pm Bug #170 (Resolved): methylC track cannot be hidden by default
fixed in v32.2.7
http://epgg-test.wustl.edu/browser/?genome=hg18&datahub_jsonfile=http://vizhub.wustl.edu/public/h...
Xin Zhou
05:22 pm Bug #173 (Resolved): coordinates jumping not working after modifying
fixed in v32.2.6 on test Xin Zhou
12:27 pm Bug #174 (Resolved): 2nd panel background color issue
fixed in v32.2.5 on test Xin Zhou

03/05/2014

10:36 pm Bug #174 (Closed): 2nd panel background color issue
* I found a minor issue, when we have set background color in main panel, after we add 2nd panel, we didn't see the b... Daofeng Li
06:08 pm Bug #172 (Resolved): methylC tracks cannot added back to secondary panels
fixed in v32.2.4 on test Xin Zhou
06:05 pm Bug #171 (Resolved): cannot load hub while showing secondary panels
fixed in v32.2.4 on test
Xin Zhou
01:30 pm Bug #173 (Closed): coordinates jumping not working after modifying
* a little bit hard to describe, please see this video: http://screencast.com/t/Vn7AfQ74y
* basically we use this re...
Daofeng Li

03/04/2014

04:58 pm Bug #172 (Closed): methylC tracks cannot added back to secondary panels
Load the browser with methylC tracks:
http://epigenomegateway.wustl.edu/browser/?genome=hg18&datahub_jsonfile=http...
Xin Zhou
02:57 pm Bug #171 (Rejected): cannot load hub while showing secondary panels
From URL parameter, create secondary panels
http://epigenomegateway.wustl.edu/browser/?genome=hg19&splinters=chr1:...
Xin Zhou

03/03/2014

11:22 pm Bug #154 (Closed): Cannot search for gene in embedded browser
Daofeng Li
11:20 pm Bug #141 (Closed): improper view range in session-restored gene set view
Daofeng Li
11:19 pm Bug #140 (Closed): error with tracks of same file URL
Daofeng Li
11:19 pm Bug #153 (Closed): track information display error
Daofeng Li
11:18 pm Bug #167 (Closed): metadata color map change not saved in session
Daofeng Li
11:16 pm Bug #169 (Closed): long range tracks not appeared in 2nd panel and also freeze 2nd panel
yes, seems the 2nd panel get working after a delay of 5 seconds here...closed. Daofeng Li
05:49 pm Bug #170 (Closed): methylC track cannot be hidden by default
methylC track cannot be hidden by default Xin Zhou
08:57 am Bug #169: long range tracks not appeared in 2nd panel and also freeze 2nd panel
yes, you are right.
I tried 3 times on Win7 last night, but didn't see this on MacOSX this morning. Will do more tes...
Daofeng Li
07:15 am Bug #169: long range tracks not appeared in 2nd panel and also freeze 2nd panel
cannot reproduce this problem on both TEST and PUBLIC
please test again and give more information
Xin Zhou

03/02/2014

11:32 pm Bug #169 (Closed): long range tracks not appeared in 2nd panel and also freeze 2nd panel
* steps I did
** load roadmap
** open 2nd panel
** load long range hub
** add IMR90 Hi-C
** see screenshot please
Daofeng Li

03/01/2014

12:59 am Bug #168 (New): 'pack and hide' status not saved in session
* the 'pack and hide' status could not be saved in session Daofeng Li

02/27/2014

11:21 am Bug #167 (Resolved): metadata color map change not saved in session
Fixed in v32.2.3 on TEST! Xin Zhou
10:57 am Bug #167 (Closed): metadata color map change not saved in session
* If I changed color of meta data color map, the setting could not be saved in session Daofeng Li
07:01 am Bug #166 (Rejected): submit default gene set error
Remove the "simplegene" track and it will be fine. Xin Zhou
12:09 am Bug #166 (Rejected): submit default gene set error
* Please see screenshot attached
Daofeng Li

02/19/2014

11:19 am Bug #165 (Closed): browser frozen when panning of BAM tracks
* Thanks for fixing! Daofeng Li
11:07 am Bug #165 (Resolved): browser frozen when panning of BAM tracks
Fixed in v32.1.8! Xin Zhou
10:15 am Bug #165 (Closed): browser frozen when panning of BAM tracks
* using this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli/C... Daofeng Li
10:13 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
Daofeng Li
10:11 am Bug #164 (Resolved): UI frozen when click 'remove all' from json hub
Fixed in v32.1.7. Thanks! Xin Zhou
09:58 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
* loading this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli... Daofeng Li

02/18/2014

03:39 pm Bug #163 (New): long responsive time while track missed in hub
* see Junchen's hub at http://remc.wustl.edu/jgu/human/remc/methylomes/methylomes_all_hub.json
* apache error log sh...
Daofeng Li
08:02 am Feature #162 (Resolved): Tooltip information
Implemented in v32.1.4. Thanks! Xin Zhou

02/15/2014

01:09 pm Bug #160 (Resolved): Custom PE BAM files unstable
Fixed in v32.1.4
http://epigenomegateway.wustl.edu/browser/?genome=danRer7&custombam=xx,http://cgs.wustl.edu/~rlow...
Xin Zhou
08:00 am Bug #153: track information display error
Missing GEO accession has been fixed. Xin Zhou

02/14/2014

10:18 pm Bug #147 (Closed): crash when track file not exist in json hub
fixed. Daofeng Li
10:17 pm Bug #153: track information display error
GEO links also could not be recovered? Daofeng Li
04:46 pm Bug #159 (Closed): Session not saving
Xin Zhou
04:45 pm Bug #155: browser url parameter for coordinate not working
Use the "native_track" keyword and add gene track to your JSON datahub.
Find example in this hub:
http://vizhub...
Xin Zhou
04:43 pm Bug #155: browser url parameter for coordinate not working
OK. I see.
Then how do I include the gene annotation track by default with my own data? When I uploaded my own tr...
Junchen Gu
04:43 pm Bug #157: refSeq gene position didn't keep in session
refSeq is a "native track". Current design only keeps order of custom tracks. Native tracks are all piled to the bottom. Xin Zhou
04:29 pm Bug #155 (Rejected): browser url parameter for coordinate not working
When the "session" and "statusId" parameters are in use, the "coordinate" parameter is disregarded, since the view ra... Xin Zhou
04:25 pm Bug #153 (Resolved): track information display error
Fixed in v32.1.3, but the track details from previous saved sessions cannot be recovered. Xin Zhou
03:58 pm Bug #147 (Resolved): crash when track file not exist in json hub
can you try again with the new code? Xin Zhou
03:31 pm Feature #162 (Closed): Tooltip information
Would be great if the tooltip could include per-read CIGAR strings, mapping quality scores, and maybe insert size inf... Rebecca Lowdon

02/13/2014

05:59 pm Feature #158: wrapping for tooltip read information
good suggestion :) Daofeng Li
05:58 pm Bug #159: Session not saving
my bad, wrong permission for the session folder. Should be fixed now. Please let me know if problem still exists. Daofeng Li
03:32 pm Feature #161 (New): Include scaffolds on genome snapshot
Would be nice to view scaffolds and unassigned chromosome fragments (in danRer7 referred to as "NA###") in the "genom... Rebecca Lowdon
03:27 pm Bug #160 (Closed): Custom PE BAM files unstable
BAM tracks of paired-end alignments appear unstable on the browser. Relocating or zooming in/out causes reads to "mov... Rebecca Lowdon
03:20 pm Bug #159 (Closed): Session not saving
Was trying to save a session to send you another bug ... but sessions not working on danRer7! Rebecca Lowdon
03:18 pm Feature #158 (New): wrapping for tooltip read information
Would be nice if information in tooltip would automatically wrap to display all information. For example, I want to v... Rebecca Lowdon

02/11/2014

10:52 pm Bug #123 (Closed): embedded browser cannot handle hidden tracks
Daofeng Li
10:52 pm Feature #145 (Closed): loose format requirement for coordinates format
* yes, it works great! Daofeng Li
10:52 pm Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive
Daofeng Li
10:51 pm Bug #148 (Closed): add geneset to genome snapshot error
Daofeng Li
10:50 pm Bug #157 (New): refSeq gene position didn't keep in session
* move refSeq gene to top of canvas
* same session, load, the refSeq gene goes to bottom
Daofeng Li

02/07/2014

11:45 pm washugb v32 release
* We have released v32 of WashU EpiGenome Browser.
h2. Updates
* shared metadata, for details please see: http:...
Daofeng Li
11:32 pm Complete Epigenome Browser Bug #156 (New): WUGB popup link get blocked
* the popup being blocked seems are default behavior of most modern browsers
Daofeng Li
04:11 pm Bug #155 (Rejected): browser url parameter for coordinate not working
Xin,
If you go to my Feb. 2014 wiki and on Feb. 6-7, I have a table of regions and in the last column there are brow...
Junchen Gu
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