>
> You can even make a page where the user clicks on a link that will
> go and post that superset url to the hgCustom or hgTracks cgi.
> Here is an example link:
> http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr11:116199665-116209156&hgt.customText=http://myserver.edu/coolSuperSetX
>
Indeed this is more or less what galaxy does to serve bigwig and bam tracks in
the proper display_application
<display id="ucsc_bigwig" version="1.0.0" name="display at UCSC">
<!-- Load links from file: one line to one link -->
<dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt"
skip_startswith="#" id="0" name="0">
<!-- Define parameters by column from file, allow splitting on builds
-->
<dynamic_param name="site_id" value="0"/>
<dynamic_param name="ucsc_link" value="1"/>
<dynamic_param name="builds" value="2" split="True" separator="," />
<!-- Filter out some of the links based upon matching site_id to a
Galaxy application configuration parameter and by dataset dbkey -->
<filter>${site_id in $APP.config.ucsc_display_sites}</filter>
<filter>${dataset.dbkey in $builds}</filter>
<!-- We define url and params as normal, but values defined in
dynamic_param are available by specified name -->
<url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
<param type="data" name="bigwig_file"
url="galaxy_${DATASET_HASH}.bigwig" strip_https="True" />
<param type="template" name="track" viewable="True"
strip_https="True">track type=bigWig name="${bigwig_file.name}"
bigDataUrl=${bigwig_file.url} db=${bigwig_file.dbkey} visibility=Full
windowingFunction=mean maxHeightPixels=128:32:11</param>
</dynamic_links>
</display>
Center for Genomic Science of IIT@SEMM
Davide Cittaro, PhD
Postdoc Senior
[email protected]
site: http://genomics.iit.it/
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