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
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>> 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>.

    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


        _____________________________________________________________
        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:

        http://lists.bx.psu.edu/


    --
    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
___________________________________________________________
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:

 http://lists.bx.psu.edu/

Reply via email to