jbrowse
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GMOD
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
JBrowse lacks any native support for customizing the main menu options above the genome browser pane—an example includes the inability for end-users to [easily] customize the “Help” menu in JBrowse....
- [ ] add another line in .travis.yml: ```SELENIUM_BROWSER=chrome JBROWSE_URL=http://localhost:9000/index.html nosetests tests/selenium_tests/``` - [ ] tweak the _getBrowser method in JBrowseTest.py - [ ] maybe rearrange the env vars a...
Do away with the paradigm of formatting scripts adding configuration during formatting. Because multiple tracks can use the same data. And the default config format should be gbrowse-like.
When data displays get very large, independently movable and scrollable panes start to get rather necessary. Should be able to move the panes independently, or link them so that they...
As things are, the GFF3 attributes `Dbxref` and `Ontology_term` are displayed in plain text in the "view details" window:  While it is possible to use `fmtDetailValue_Dbxref` and `fmtDetailValue_Ontology_term` with...
With the [GBrowse_img](http://gmod.org/wiki/GBrowse_img) component of [GBrowse](http://gmod.org/wiki/Gbrowse), we had the ability to export any region and track(s) to an external web page. The regions could be embedded as an image via...
It would be convenient if JBrowse could render spliced alignments from tabix-indexed GFF3 files using the CIGAR string in the GFF3 Gap attribute (e.g., produced from gmap's gff3_match_est format), rather...
Adding track-level permissions to JBrowse tracks in Apollo and JBrowse directly. Item 8 in GMOD Hackathon http://gmod.org/wiki/2018_PAG_Hackathon Ref: https://github.com/GMOD/Apollo/issues/17 This feature that is generally already capable to some extent by...
Hi, I wanted to change the colour (and if possible also the length) of the arrows indicating the direction of features in a Canvas track. I tried modifying the files...
There are more than 1500 servers for annotations. It could be beneficial to add them to JBrowse. Info on DAS: http://www.biodas.org/wiki/Main_Page The list of existing servers: http://www.dasregistry.org/listSources.jsp
