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...

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/

---

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/