Ucsc bigbed display tool does not show up on local installation
Hello: The display tool for UCSC that comes with the local installation package does not work. uploading a bigbed file (from the test-data that comes with the package) does not trigger the webapp to show an option to view the file using UCSC's viewer. How do I enable this ? To reproduce the issue, simply download galaxy using mercurial. change the host address to 0.0.0.0. and load the bigbed file from the test-data directory. Once the file uploads, the user should expect to see a display tool added to the files description (on the right), but nothing is shown. Thanks Jeremy UNCC
Hello Jeremy, Galaxy does not come with a display tool for UCSC. There is an integrated display tool, under Visualization, commonly called "Trackster". The icon for Trackster is a set of colored, stacked bars that when hovered over is labeled "Visualize in Trackster". If you do want to display at the public (or a local mirror) UCSC browser, then some additional set-up is required. Here are the links to the details, including a tutorial: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy (scroll to Display at UCSC) http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tu... http://wiki.g2.bx.psu.edu/Admin Hopefully this helps to get you started, Jen Galaxy team On 11/2/11 3:52 PM, Jeremy Villalobos wrote:
Hello:
The display tool for UCSC that comes with the local installation package does not work. uploading a bigbed file (from the test-data that comes with the package) does not trigger the webapp to show an option to view the file using UCSC's viewer.
How do I enable this ?
To reproduce the issue, simply download galaxy using mercurial. change the host address to 0.0.0.0. and load the bigbed file from the test-data directory. Once the file uploads, the user should expect to see a display tool added to the files description (on the right), but nothing is shown.
Thanks
Jeremy UNCC
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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Thanks for your response. I figured out it was some extra text at the end of the xml file that was preventing galaxy from reading the file. I also was confused about how to setup the proxy. For Ubuntu, the apache2 configuration file is in /etc/apache2/sites-available/default (using virtual servers by default) I was initially working with /etc/apache2/httpd.conf which I think may be the standard in other distros. Jeremy On Thu, Nov 3, 2011 at 7:23 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Jeremy,
Galaxy does not come with a display tool for UCSC. There is an integrated display tool, under Visualization, commonly called "Trackster". The icon for Trackster is a set of colored, stacked bars that when hovered over is labeled "Visualize in Trackster".
If you do want to display at the public (or a local mirror) UCSC browser, then some additional set-up is required. Here are the links to the details, including a tutorial:
http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxy<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy>(scroll to Display at UCSC)
http://wiki.g2.bx.psu.edu/**Admin/Tools/External%** 20Display%20Applications%**20Tutorial<http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial>
http://wiki.g2.bx.psu.edu/**Admin <http://wiki.g2.bx.psu.edu/Admin>
Hopefully this helps to get you started,
Jen Galaxy team
On 11/2/11 3:52 PM, Jeremy Villalobos wrote:
Hello:
The display tool for UCSC that comes with the local installation package does not work. uploading a bigbed file (from the test-data that comes with the package) does not trigger the webapp to show an option to view the file using UCSC's viewer.
How do I enable this ?
To reproduce the issue, simply download galaxy using mercurial. change the host address to 0.0.0.0. and load the bigbed file from the test-data directory. Once the file uploads, the user should expect to see a display tool added to the files description (on the right), but nothing is shown.
Thanks
Jeremy UNCC
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/**Support<http://galaxyproject.org/wiki/Support>
participants (2)
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Jennifer Jackson -
Jeremy Villalobos