Hi Anton and the galaxy group, Tests of the ENCODEdb connection on the galaxy test site as Anton suggested generates this new set of errors: -------- URL: http://test.g2.bx.psu.edu:9001/async/encode_db1 Module paste.exceptions.errormiddleware:138 in __call__ Module paste.lint:65 in lint_app Module flup.middleware.session:743 in __call__ Module paste.recursive:54 in __call__ Module paste.httpexceptions:619 in __call__ Module paste.wsgilib:112 in catch_errors_app Module galaxy.web.framework:104 in __call__ << kwargs = trans.request.params.copy() kwargs.update( map ) body = method( trans, **kwargs ) # Now figure out what we got back and try to get it to the browser in # a smart way >> body = method( trans, **kwargs ) Module galaxy.interfaces.async:85 in index << GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17' data = datatypes.factory(ext=GALAXY_TYPE)() data.ext = GALAXY_TYPE data.name = GALAXY_NAME>> data = datatypes.factory(ext=GALAXY_TYPE)() exceptions.AttributeError: 'module' object has no attribute 'factory' -------- Thanks Prachi

-----Original Message----- From: Elnitski, Laura (NIH/NHGRI) [E] [mailto:elnitski@mail.nih.gov] Sent: Wednesday, June 28, 2006 3:16 PM To: prachi@stanford.edu; Umayam, Lowell (NIH/NHGRI) [C] Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] Subject: Thanks for the answer

FYI- here's the response from Anton

-----Original Message----- From: Anton Nekrutenko [mailto:anton@bx.psu.edu] Sent: Wed 6/28/2006 5:38 PM To: Elnitski, Laura (NIH/NHGRI) [E] Cc: galaxy-user@bx.psu.edu Subject: Re: [Galaxy-user] FW: Fwd: Fw: FW: Is Galaxy down?

The Encode db datasource was not loaded into running galaxy. It is corrected now and running at http://test.g2.bx.psu.edu

Use this URL for testing and let us know.

anton

Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

On Jun 28, 2006, at 5:07 PM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote:

...

Hi-

thanks for your help. the message below shows another error we're getting. Normally, we'd take more time to investigate the problem before asking you, but our manuscript is out for review right now and we need resolution of this ASAP. If you think it can only be handled on our end, let me know, but if you have suggestions for the fix- we would greatly appreciate hearing them.

Thanks again, Laura

-----Original Message----- From: Umayam, Lowell (NIH/NHGRI) [C] Sent: Wed 6/28/2006 5:02 PM To: Elnitski, Laura (NIH/NHGRI) [E]; prachi@stanford.edu Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] Subject: Re: Fwd: Fw: [Galaxy-user] FW: Is Galaxy down?

Hi Laura, Switched the URL so it's pointing to the correct public port. So now it's getting access to the galaxy server but now another error has developed. It looks like they must have changed the script on their end and that it's now taking different arguments. This error is out of my scope since I really don't have any expertise with the scripts on Galaxy. I think Prachi should look into this.

-Lowell

Server Error

URL: http://g2.bx.psu.edu:8085/async/encode_db1 Module paste.exceptions.errormiddleware:*138* in |__call__| Module paste.lint:*65* in |lint_app| Module flup.middleware.session:*743* in |__call__| Module paste.recursive:*54* in |__call__| Module paste.httpexceptions:*619* in |__call__| Module paste.wsgilib:*112* in |catch_errors_app| Module galaxy.web.framework:*104* in |__call__| |<< <http://g2.bx.psu.edu:8085/async/encode_db1#> kwargs *=* trans*.*request*.*params*.*copy*(**)* kwargs*.*update*(* map *)* body *=* method*(* trans*,* ****kwargs *)* # Now figure out what we got back and try to get it to the browser in # a smart way ||>> <http://g2.bx.psu.edu:8085/async/encode_db1#>body *=* method*(* trans*,* ****kwargs *)*| *exceptions.TypeError: default() takes at least 3 non-keyword arguments (2 given)

*

Tyra Wolfsberg wrote:

...

...

Subject: Fw: [Galaxy-user] FW: Is Galaxy down? Date: Wed, 28 Jun 2006 16:04:56 -0400 Thread-Topic: [Galaxy-user] FW: Is Galaxy down? Thread-Index: Acaau6b4nybF168GSgeMfrMVI4hHmAAMnsjC From: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski@mail.nih.gov> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <tyra@nhgri.nih.gov>

Hi can you forward this to Lowell? I'm in italy :-) Laura -------------------------- Sent from my BlackBerry Wireless Device

----- Original Message ----- From: Nate Coraor <nate@bx.psu.edu> To: Elnitski, Laura (NIH/NHGRI) [E] Cc: galaxy-user@bx.psu.edu <galaxy-user@bx.psu.edu> Sent: Wed Jun 28 10:04:35 2006 Subject: Re: [Galaxy-user] FW: Is Galaxy down?

On Jun 28, 2006, at 7:49 AM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote:

...

Can you give us any guidance on our ENCODEdb connection problem?

Laura,

It's on port 8885, although the "public" interface is now just:

<http://main.g2.bx.psu.edu/>http://main.g2.bx.psu.edu/

--nate

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