[Galaxy-user] FW: Fwd: Fw: FW: Is Galaxy down?

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[Galaxy-user] FW: Fwd: Fw: FW: Is Galaxy down?

Laura Elnitski

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]; [hidden email]
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]" <[hidden email]>
>> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <[hidden email]>
>>
>> Hi can you forward this to Lowell? I'm in italy :-)
>> Laura
>> --------------------------
>> Sent from my BlackBerry Wireless Device
>>
>>
>> ----- Original Message -----
>> From: Nate Coraor <[hidden email]>
>> To: Elnitski, Laura (NIH/NHGRI) [E]
>> Cc: [hidden email] <[hidden email]>
>> 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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Re: FW: Fwd: Fw: FW: Is Galaxy down?

Anton Nekrutenko
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
[hidden email]
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]; [hidden email]
> 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]" <[hidden email]>
>>> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <[hidden email]>
>>>
>>> Hi can you forward this to Lowell? I'm in italy :-)
>>> Laura
>>> --------------------------
>>> Sent from my BlackBerry Wireless Device
>>>
>>>
>>> ----- Original Message -----
>>> From: Nate Coraor <[hidden email]>
>>> To: Elnitski, Laura (NIH/NHGRI) [E]
>>> Cc: [hidden email] <[hidden email]>
>>> 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
>>
>>
>
>
> _______________________________________________
> Galaxy-user mailing list
> [hidden email]
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user


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Re: FW: Fwd: Fw: FW: Is Galaxy down?

Laura Elnitski
Thanks very much!

Laura


-----Original Message-----
From: Anton Nekrutenko [mailto:[hidden email]]
Sent: Wed 6/28/2006 5:38 PM
To: Elnitski, Laura (NIH/NHGRI) [E]
Cc: [hidden email]
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
[hidden email]
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]; [hidden email]
> 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]" <[hidden email]>
>>> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <[hidden email]>
>>>
>>> Hi can you forward this to Lowell? I'm in italy :-)
>>> Laura
>>> --------------------------
>>> Sent from my BlackBerry Wireless Device
>>>
>>>
>>> ----- Original Message -----
>>> From: Nate Coraor <[hidden email]>
>>> To: Elnitski, Laura (NIH/NHGRI) [E]
>>> Cc: [hidden email] <[hidden email]>
>>> 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
>>
>>
>
>
> _______________________________________________
> Galaxy-user mailing list
> [hidden email]
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user