Hi James, 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, Dan 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 > /tool_runner/test_me?type=text&name=Homo%20sapiens%20genes%20(GRCh37.p5)&URL=http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1&resultsButton=1 > HTTP/1.1" 302 - > "http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101 > Firefox/8.0.1" > > 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, > -James > > 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, > > Dan > > > > On Dec 1, 2011, at 5:08 AM, James Ireland wrote: > >> Greetings, >> >> 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! >> -James >> >> >> -- >> 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" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > > > > -- > J Ireland > www.5amsolutions.com | Software for Life(TM) > m: 415 484-DATA (3282) > <test_me.xml>
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