Hello Colin,
There are a few things to double check:
1 - database has been assigned and that database is an existing UCSC
Genome Browser genome. You can double check this at http://genome.ucsc.edu
2 - dataset file type is set as BAM, resulting in a dataset extension
".bam". Most likely this is already the case, if the Ensembl link works
(is not simply displayed, but the data displays there successfully). If
display remains and issue, one way to ensure that there are no
formatting issues (missing .bai index, etc.). is to load the original
SAM file and convert within Galaxy using the SAM->BAM tool, if you have
not tried this already.
Both 1 & 2 can be set using the "Edit Attribute" function (click on
pencil icon in the top right corner of the dataset box).
3 - Perhaps the UCSC link-up needs to be configured again?
A new tutorial is here:
https://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/Tutorial
And in the Apache set-up wiki, the section "Display at UCSC" has the
details. This is likely what you set-up previously when the link was
successful:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
4 - Another final way to trouble-shoot is to load the data into Galaxy
main (ideally SAM load, then run SAM->BAM, assign database if needed)
and see if the link/load to UCSC is successful. If it works, then we can
narrow this down to a data loading or configuration issue in your
instance. If it doesn't work at Galaxy main, then we can probably assume
this is a dataset issue, so please send a direct bug report using the
green bug icon (bottom left of dataset box) and we can try to offer more
assistance using that information (actual data, etc.) as it provides the
most direct access to the history/dataset. I'll watch for a bug report
linked to this issue. It would be helpful if you could note in the
comments that this is you and the same issue, should the Galaxy account
you are using for this has a different associated email address.
Hopefully one of these will root out the issue & we can get it resolved
quickly.
Best,
Jen
Galaxy team
On 7/3/11 10:19 PM, colin molter wrote:
Hello all,
sorry for the very basic question (I tried to find some answer on the
mailing list or faq but without any success).
So here is my problem:
i installed a fresh copy of galaxy in my server with apache.
everything looks fine (i managed to perform several analyses so far).
The problem is that there is *no link to UCSC*!!
For my BAM file, i just have:
display at Ensembl Current
<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl_interval/ensembl_Current>
And for the pileup: view in GeneTrack
<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/genetrack_interval/genetrack>
display at Ensembl Current
<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl_interval/ensembl_Current>
any idea bout how to have this link back.
thks again
colin
--
Colin Molter
University of Brussels - InSilico Team - http://insilico.ulb.ac.be/
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--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
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