Re: [galaxy-dev] No Display at UCSC Main link.

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 <yangluob@isu.edu mailto:yangluob@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 <jen@bx.psu.edu
<mailto:jen@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
        <jen@bx.psu.edu <mailto:jen@bx.psu.edu>
        <mailto:jen@bx.psu.edu <mailto:jen@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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    http://galaxyproject.org/wiki/__Support
    <http://galaxyproject.org/wiki/Support>