For legacy reasons, Biomart uses a special-cased GALAXY_URL parameter, which is
likely the source of the problem. If you remove the '<param name="GALAXY_URL"
... />' input parameter, restart Galaxy and reload the Galaxy interface, does
it then work correctly?
Thanks for using Galaxy,
On Dec 1, 2011, at 11:18 AM, James Ireland wrote:
> Hi Dan,
> Thanks for the quick response!
> I have a feeling this is something silly that I'm missing. As a reality
> check I simply created a copy of the biomart.xml tool.xml file and called it
> test_me.xml. I changed the tool_id and GALAXY_URL in the xml file as you'll
> see and added a link in my tool_config. Selecting this tool from the Get
> Data folder brings me to Biomart as expected. When I hit "go", I have the
> same issue of just being redirected to the welcome page. The server output
> is shown below. The unchanged biomart tool continues to work fine.
> Galaxy server output:
> 127.0.0.1 - - [01/Dec/2011:08:08:27 -0700] "POST
> HTTP/1.1" 302 -
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101
> Here's my Galaxy revision info:
> changeset: 6056:338ead4737ba
> tag: tip
> user: Nate Coraor <n...@bx.psu.edu>
> date: Thu Sep 29 16:45:19 2011 -0400
> Thanks again,
> P.S. It's my pleasure to use Galaxy! ;)
> On Thu, Dec 1, 2011 at 7:06 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi James,
> Can you let us know which revision of Galaxy that you are using (hg head) and
> any log output that appears when accessing or running the tool? Also the list
> of parameters and values that are being POSTed to Galaxy and a copy of your
> tool.xml file would be useful.
> Thanks for using Galaxy,
> On Dec 1, 2011, at 5:08 AM, James Ireland wrote:
>> I've been attempting to return data to Galaxy via the synchronous data
>> depositing protocol. Using the Biomart, UCSC Table Browser, etc as examples
>> in the data_source tools directory, I've been able to get the initial GET
>> request to my site just fine. However, when I POST back to galaxy I
>> immediately get a redirect to the welcome page and Galaxy never resubmits
>> back to my site.
>> I was wondering if there is more to the protocol than is covered here:
>> http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources or perhaps
>> configuration I need to perform on my local Galaxy installation to correctly
>> handle the POSTs back to tool_runner? Also, are there any code examples I
>> should be looking at?
>> Thanks for your help!
>> J Ireland
>> www.5amsolutions.com | Software for Life(TM)
>> m: 415 484-DATA (3282)
>> Please keep all replies on the list by using "reply all"
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> J Ireland
> www.5amsolutions.com | Software for Life(TM)
> m: 415 484-DATA (3282)
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