Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

[Predeus, O. <A.P...@li...>]

Dear Colin, thank you very much for your help!


All of your suggestions are extremely helpful.


>  I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.


We are processing a large bunch of RNA-seq conditions in bacterial strains. Genomes and annotations are not huge so having e.g. 40-60 tracks does not slow it down too much. At the same time, people quite often need to look at all replicates and conditions. This means they have to click on 60 checkboxes, which is not ideal, of course.


Thank you again!


-- Alex

________________________________
From: Colin <col...@gm...>
Sent: Monday, November 19, 2018 1:31:48 PM
To: Predeus, Olexandr
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

1. It is true that faceted allows the shift-select of multiple tracks but sort of has that arbitrary limit. Hierarchical track selector has a plugin for multiple select that could help https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard coded limit could be removed. I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.

2. There are several options for tracks to load by default `defaultTracks`, `forceTracks`, and `alwaysOnTracks`. Example `defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note: defaultTracks is overridden by cookies/previous sessions, and forceTracks is overridden by URL lists of tracks, and alwaysOnTracks always loads the tracks, so kind of three levels of forcing the track to be displayed.

3. There aren't really very great hooks to add logos and such presently. For a really hacky solution you could just add some extra script

    <script>
var timer = setInterval(() => {
    var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
    if(ret) {
        var img = document.createElement('img')
        img.src = 'yourlogo.png'
        ret.prepend(img)
        clearInterval(timer)
    }
},200)
    </script>


4. The categoryOrder config was added recently for ordering the categories of the hierarchical track selector. If you have more details on the case please describe further. There is also "sortHierarchical: false" option where there is no sorting applied and the order is just based on the order of the tracks in the trackList.json/tracks.conf


-Colin

On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <A.P...@li...<mailto:A.P...@li...>> wrote:

Hello all,


I was wondering several things about JBrowse configuration I couldn't figure out after searching the manual.


  1.  Is there an option or selecting all the tracks at once? Maybe a plugin? I've tried faceted selection, but that doesn't allow you to do more than 30, and all of my datasets do have more. And it's quite inconvenient to click on them too. So I'd appreciate any suggestions.
  2.  How can I set up which files are selected upon loading the dataset? E.g. if I want half of the tracks to be selected to begin with?
  3.  Is there any way to customize the dataset selector screen? E.g. add a picture or some other links?
  4.  How can I change the order of tracks within each category? I managed to sort categories by adding a number to their name - do I have to do the same with the keys?

Thank you very much in advance!

-- Alex

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