Hello Luobin,

Thanks for sending the additional information. It sounds as if you are using the default version of:
tool-data/shared/ucsc/ucsc_build_sites.txt

Adding hg19 to "main" in this file will add the link to the datasets.

Hopefully this helps,

Best,

Jen
Galaxy team

On 2/17/12 1:58 PM, Luobin Yang wrote:
Hi, Jen,

I noticed that when I use hg18 or other database builds, the UCSC
display link shows up, but when I use hg19 database builds, there is no
UCSC display link.

Thanks,
Luobin

On Wed, Feb 15, 2012 at 11:30 AM, Luobin Yang <yangl...@isu.edu
<mailto:yangl...@isu.edu>> wrote:

    Hi, Jen,

    Thanks for your replay. Yes, it's an instance that I installed here
    at ISU, not the main instance at PSU. The dataset is BED and the
    database is hg19.

    In my universe_wsgi.ini file, I have the following lines:
    # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
    ucsc_display_sites = main,test,archaea,ucla

    In my apache configuration file, I added the following:

      
<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1c9ec50d26246b3120bb238_1><Location
  "/root/display_as">
      
<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1c9ec50d26246b3120bb238_2>
    Satisfy  Any

           Order  deny,allow
           Deny  fromall
           Allow  fromhgw1.cse.ucsc.edu  <http://hgw1.cse.ucsc.edu>
           Allow  fromhgw2.cse.ucsc.edu  <http://hgw2.cse.ucsc.edu>
           Allow  fromhgw3.cse.ucsc.edu  <http://hgw3.cse.ucsc.edu>
           Allow  fromhgw4.cse.ucsc.edu  <http://hgw4.cse.ucsc.edu>
           Allow  fromhgw5.cse.ucsc.edu  <http://hgw5.cse.ucsc.edu>
           Allow  fromhgw6.cse.ucsc.edu  <http://hgw6.cse.ucsc.edu>
           Allow  fromhgw7.cse.ucsc.edu  <http://hgw7.cse.ucsc.edu>
           Allow  fromhgw8.cse.ucsc.edu  <http://hgw8.cse.ucsc.edu>
      </Location>


    One thing I would like to ask you about is for above Apache
    configuration, because my Galaxy is served as /galaxy subdirectory
    instead of the root directory, do I need to make changed to above
    location? for instance, instead of "/root/display_as", use
    "/galaxy/root/display_as" ?

    Thanks so much!
    Luobin


    On Tue, Feb 14, 2012 at 10:51 PM, Jennifer Jackson <j...@bx.psu.edu
    <mailto:j...@bx.psu.edu>> wrote:

        Hello again,

        The link is not a Galaxy Main public instance share link, which
        would start with: http://main.g2.bx.psu.edu

        Having the datatype as BED and the database as hg19 would (for
        all of the cases I can think of) bring up the "View at UCSC"
        link, if the instance is set up to have "display at UCSC"
        configured.

        So, the root cause of the problem is probably with how this
        other instance is set up. If this is not your instance, you will
        want to contact the folks running it to see if they have plans
        to configure UCSC display. If this is yours, follow the
        instructions on this wiki to get set up:

        http://wiki.g2.bx.psu.edu/__Admin/Config/Apache%20Proxy
        <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy>
        See the section: Display at UCSC

        Hopefully this helps,

        Best,

        Jen
        Galaxy team



        On 2/14/12 9:26 PM, Luobin Yang wrote:

            Hi, Jen,

            The dataset is BED datatype and the database is hg19.
            Actually this
            history contains the same steps as those in Galaxy101 tutorial.

            I created the link for the history and here it is:

        XXXXXXXXXXXXXXXXXXXXXXXXXXXX


            So basically I do not see an option called "Display at UCSC
            Main", but
            it has two other options, "View in GeneTrack" and "Display
            at Ensemble
            Current"

            Thanks,
            Luobin

            On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson
            <j...@bx.psu.edu <mailto:j...@bx.psu.edu>
            <mailto:j...@bx.psu.edu <mailto:j...@bx.psu.edu>>> wrote:

                Hi Luobin,

                To display at UCSC, the datatype has to be a UCSC
            display type and
                the database has to be a UCSC genome browser. Often,
            small changes
                can be made to tune a dataset to help it fit into these
                requirements. Other times, a dataset will need to be
            transformed
                into another type or it can't be viewed at all because
            the genome is
                not available at UCSC.

                You should try to modify these attributes yourself
            first. Common
                UCSC datatypes from Galaxy are: BED, bigBED, BAM. For
            the list of
                UCSC known datatypes, see:
            http://genome.ucsc.edu/FAQ/____FAQformat.html
            <http://genome.ucsc.edu/FAQ/__FAQformat.html>
            <http://genome.ucsc.edu/FAQ/__FAQformat.html
            <http://genome.ucsc.edu/FAQ/FAQformat.html>>.


                Known databases would be any that you also can find at:
            http://genome.ucsc.edu as full genome assemblies. The short
            label
                used at UCSC should match the database assignment at
            Galaxy. For
                example, the most recent human would be "hg19" at both.

                If you are still stuck and would like to send me a
            shared history
                link, I can provide feedback about how to modify (if
            possible) to
                view at UCSC. Use "Options -> Share or Publish",
            generate the link,
                and email this link directly back to me. Be sure to
            include the
                dataset #, so that I know which in your history you want
            to view at
                UCSC.

                Best,

                Jen
                Galaxy team


                On 2/14/12 11:50 AM, Luobin Yang wrote:

                    Hi,

                    I have a local instance of Galaxy, but I found there
            is no
            "Display at
                    UCSC Main" link for some datasets that can be viewed
            in GeneTrack or
                    displayed by Ensemble, what has been wrong?

                    Thanks,
                    Luobin



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                --
                Jennifer Jackson
            http://usegalaxy.org
            http://galaxyproject.org/wiki/____Support
            <http://galaxyproject.org/wiki/__Support>
            <http://galaxyproject.org/__wiki/Support
            <http://galaxyproject.org/wiki/Support>>



        --
        Jennifer Jackson
        http://usegalaxy.org
        http://galaxyproject.org/wiki/__Support
        <http://galaxyproject.org/wiki/Support>




--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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