[InterMine Dev] [Fwd: Exporting data to Galaxy]

Lewis, Brian Andrew brilewis at iupui.edu
Tue Sep 6 15:26:37 BST 2011


It is 0.97, which is the latest version.

~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Tuesday, September 06, 2011 10:17 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Hi Brian,

Based on the fact that you can actually send intermine data to Galaxy and the URL value is null, it should be an intermine issue. It looks to me you are working with a fairly old version of intermine, what version is it?

Cheers
Fengyuan

On 06/09/11 15:08, Lewis, Brian Andrew wrote:
Fengyuan -

I just checked and it looks like the 'URL' field is not being generated correctly (see attached image) since the value is blank.  Unfortunately the server isn't public, so I can't give you the URL.  I did attach my intermine.properties file as well, with some server details removed.

I did create a new data source tool for Galaxy and it is pointing to the correct URL of our InterMine instance.

Because of the nature of the issue, I really wasn't sure if this was a question for Galaxy's dev mailing list or InterMine's.

Thanks,
~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Monday, September 05, 2011 8:23 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org<mailto:dev at intermine.org>
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Dear Brian,

Sorry for the slow reply.

First of all, it seems you've set up galaxy config in InterMine the right way. I've tried to reproduce your error, but it works fine for me to send data from a local InterMine to a local Galaxy.

The "URL" content should be programmatically generated by InterMine. Is your server public for me to test on? Or can you inspect it by firebug in firefox or chrome on the export page, there should be a hidden field called "URL" (see screenshot attached). Can you find it in your page? A further question is, did you create a new data_souce tool<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ctool.3E_tag_set>  for your mine or you are using an existing tool, such as modmine or flymine, etc. (this is set in web.properties as for "galaxy.url.value" key)?

I've also checked the source code for Galaxy data_source (galaxy-dist/tools/data_souce/data_source.py) , the error is indeed caused by the missing "URL" parameter in the http request. It looks quite odd to me so far.

Thanks
Fengyuan

On 05/09/11 10:39, julie at flymine.org<mailto:julie at flymine.org> wrote:

---------------------------- Original Message ----------------------------

Subject: [InterMine Dev] Exporting data to Galaxy

From:    "Lewis, Brian Andrew" <brilewis at iupui.edu><mailto:brilewis at iupui.edu>

Date:    Fri, September 2, 2011 6:53 pm

To:      "dev at intermine.org"<mailto:dev at intermine.org> <dev at intermine.org><mailto:dev at intermine.org>

--------------------------------------------------------------------------



I'm in the process of hooking up our instance of InterMine to an instance

of Galaxy (on the same server).  I figured out that I need to added the

section to tiles-defs-model.xml and modify the web.properties file as

well.  After re-deploying my mine, I'm able to get to the "Export to

Galaxy" page.  When I click "Export", the job does go to Galaxy but I get

the following error message back from Galaxy:



An error occurred running this job: The remote data source application has

not sent back a URL parameter in the request.



To anyone with experience hooking up these two apps, could you let me know

how to set this URL parameter?



Thanks,

Brian Lewis

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