= xQTL GBrowse integration =

Proposed is that if a user want to view data on a gBrowse the following happens
* Produce a BigBed (for annotations such as Marker) / BigWig files (for decimal data such as QTL). This may take some time on first call, or if the files needs refreshing on change
* Include in MOLGENIS suitable links towards the gBrowse instance that include loading of that custom track
* Include in these files hyperlinks back to the molgenis instance
See http://bioinformatics.oxfordjournals.org/content/26/17/2204.full.pdf
== How to add GBrowse linkouts to MOLGENIS databases ==

=== Add a query option to the 'rubberband' menu where you can drag to select a genomic region ===

Open your GBrowse *.conf file. The rubberband menu has HTML elements and looks like this:

{{{
[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr>
           <th style="background:lightgrey;cell-padding:5">
             SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
                   onclick="SelectArea.prototype.cancelRubber()">
               [X]
             </span>
           </th>
         </tr>
}}}

We add a table row with the linkout to a URL like this:

{{{
<tr>
  <td onmouseup="SelectArea.prototype.cancelRubber()">
    <a href="http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=SELECTION" target="_BLANK">
    molgenis region query
    </a>
  </td>
</tr>
}}}

The value of SELECTION is a GBrowse notation, so the accepting service must be compatible with these requests. An example of a resulting request:

{{{
.../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999
}}}

At the moment there is no MolgenisService to facility this, but it the principles are trivial. [http://www.molgenis.org/changeset/9697 A first step was done] to enhance the existing filters for this purpose, but this is not GBrowse syntax yet. The multifilters [http://localhost:8080/xqtl/molgenis.do?__target=Markers&__action=filter_set&__filter_attribute=Marker_bpstart&__filter_operator=GREATER&__filter_value=15&__filter_attribute1=Marker_bpstart&__filter_operator1=LESS&__filter_value1=35 are used like this].

=== Add a popup balloon to an annotation track ===

Open your GBrowse *.conf file. In the track, which e.g. looks like this:

{{{
[hxb-sdp]
feature       = experimental_feature:hxb_sdp
database      = variations
}}}

We add a `balloon` property, with a hyperlink, like this:

{{{
balloon click = <h2>Marker $name</h2>
       <a href='http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=$id'>Marker info from molgenis</a><br>
}}}

When clicking this link, it will request a marker by ID. The correct mapping for the $-variable to MOLGENIS entity attribute should be investigated on a per-database basis.

{{{
.../api/find/org.molgenis.xgap.Marker?name=1
}}}

== Online GBrowse at GWAS Central (HGV-Base) ==

http://www.gwascentral.org/browser/genome?r=HGVRS1375,HGVRS1374,HGVRS1373&t=

== Online GBrowse at WormBase ==

http://www.wormbase.org/db/gb2/gbrowse/c_elegans/?name=I:10747696..10779324