Add the trackhub composite datatype #2348
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| <display id="ucsc_huba" version="1.0.0" name="display at Track Hub UCSC"> | |||
| <link id="main" name="main"> | |||
| <url>https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=${qp($hub_file.url + '/myHub/hub.txt')}&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on</url> | |||
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Should this be configurable?
There are many UCSC instances which could be used.
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I will be happy to set this configurable, how do we set this up?
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@remimarenco good to start a day with such a great idea! Thanks a lot! |
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Thanks for all the reviews @bgruening and @dannon! Will take care of this soon :) |
…uba.xml to trackhub.xml, changed iteritems to items, removed hubAssembly.py to port it into tracks.py
…g of the datatype/its use in Galaxy
remimarenco
changed the title
Typo in the extension
Remove blank lines in file.
| <display id="ucsc_trackhub" version="1.0.0" name="display at Track Hub UCSC"> | ||
| <link id="main" name="main"> | ||
| <url>https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=${qp($hub_file.url + '/myHub/hub.txt')}&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on</url> | ||
| <param type="data" name="hub_file" url="galaxy_${DATASET_HASH}" allow_extra_files_access="True" strip_https="True"/> |
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Is strip_https="True" actually needed here?
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I just followed the wiki about this.
What is advised for this / what are the cases?
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It swaps https to http (when Galaxy is under https) for the url that Galaxy gives to the external display application. At one point the UCSC genome browser was not able to fetch https URLs; I do not think this is the case any longer.
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Ok perfect! I will change also that on the wiki then?
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@galaxybot test this |
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Thanks @remimarenco - good luck with G-OnRamp. Any progress on testing composite datatypes? |
Fix unaddressed comments from galaxyproject#2348.
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@jmchilton This was merged with 3 unaddressed comments, see #2646. |
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@jmchilton @nsoranzo Thank you for taking care of this. (Yes @jmchilton, workshop about it tomorrow, for two days! Exciting :) ) |
Hi!
Some of you are maybe aware we are building, at goeckslab, a workflow for genome annotation which is very tied with Galaxy: G-OnRamp.
One of the tools of G-OnRamp workflow is called HubArchiveCreator and allows to visualize tracks generated inside Galaxy, onto UCSC TrackHub.
To enable this, I needed to add a datatype, and a display_application.
With @jgoecks, we though it could be really useful to have TrackHub UCSC / G-OnRamp compatibility being directly available on Galaxy installation, so here is the PR :).
Here is a print screen of the result:
To test the datatype:
dbia3_trfBig_sorted.bed.txt
dbia3.fa.txt
(Remove the .txt extension => GitHub does not accept
.faor.bed)dbia3.faasreference genomeand:trfBig.bedThis image might help:
And you're done! You have huba datatype installed, and you can visualize:
files into UCSC TrackHub :)