[biomart-users] Re: [Ensembl #177537] Re: Problem with server

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[biomart-users] Re: [Ensembl #177537] Re: Problem with server

Arek Kasprzyk
Hi Kevin,

(Moving this discussion back to the BioMart mailing list).

I could not see anything specific in your error log. I decided therefore to repeat exactly your steps and did not run into any problems. Please see below:


Inline images 1
Clicking on the config brings the default query form as expected:

Inline images 2



Finally, executing the query with all attributes checked, seems to work fine too


Inline images 3


I am running my BioMart on MacOS Sierra 10.12.3


a.












On 9 March 2017 at 10:46, Benjamin Moore via RT <[hidden email]> wrote:
Dear Kevin,

I believe your question is better directed to the BioMart community. It seems
that Arek has helped you on the BioMart mailing list. I'm only really able to
help with problems relating to the Ensembl BioMart. I will now close this
ticket from the Ensembl Helpdesk. Please also remove [hidden email] in
any future replies so that our e-mail system isn't confused!

Best wishes

Ben
Ensembl Helpdesk

On Wed Mar 08 18:53:10 2017, [hidden email] wrote:

  Dear all

  Thanks for the feedback.

  I add the steps with images and the log to know if I am having an error
  when running the server and to be able to receive help.

  Yours sincerely.


   


   

  MTI Kevin Alquicira Hernández

  Programa de Genómica Computacional

  Centro de Ciencias Genómicas / UNAM

  Av. Universidad s/n Col. Chamilpa 62210,

  Cuernavaca, Mor. Tel. (01)777-3132063

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

  De: Arek Kasprzyk <[hidden email]>
  Enviado: martes, 7 de marzo de 2017 02:35 a. m.
  Para: Kevin Alquicira
  Cc: [hidden email]
  Asunto: Re: Problem with server Hi Kevin, I must have missed your initial
  email somehow. I have replied just now to your email on the BioMart mailing
  list. a. On 7 March 2017 at 02:44, Kevin Alquicira <
  [hidden email] (mailto:[hidden email])> wrote:

    Hi

    Please can you help me (It is very important to me)?

    I get the following error when I run the server...

    I followed the manual instructions (http://www.biomart.org/other/biomart_0.9_0_documentation.pdf):

     [1]BioMart 0.9.0 User Manual[2]www.biomart.org10 You will be prompted
    to save the registry file you’ve created, and after doing so the
    server will be deployed on your local machine, port 9000.



    1. http://www.biomart.org/other/biomart_0.9_0_documentation.pdf
    2. http://www.biomart.org

    - Page 9
    To test the registry you can now click on the Start Server button in
    the upper-right...

    I use os x el capitan.

    Sorry but I have no response in the forum.

    https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM

     [1][IMAGE]                                                               [1]An error has occurred on the server...?[2]groups.google.comPosted
                                                                             24/02/17 03:03


    1. https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM
                                                                             1. https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM
                                                                             2. http://groups.google.com

    Thank you very much


     


     

    MTI Kevin Alquicira Hernández

    Programa de Genómica Computacional

    Centro de Ciencias Genómicas / UNAM

    Av. Universidad s/n Col. Chamilpa 62210,

    Cuernavaca, Mor. Tel. (01)777-3132063



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[biomart-users] Re: [Ensembl #177537] Re: Problem with server

Arek Kasprzyk
Hi Kevin,

the log that you want is here: BioMart/dist/logs. Look for stdouterr.
You need to install everything following the instructions on http://www.biomart.org/download.html.
Please remember to use the correct java version

a.

On 15 March 2017 at 03:57, Kevin Alquicira <[hidden email]> wrote:

Dear Arek


Many thanks for your response.

I continue with the same problem, I think it may be due to the installation of biomart, 

To install ant i use brew. Should you install in a special way and specific version?

Is there another different log from the terminal?

I installed biomart on another computer and followed the same steps ... but I have the same problem.


Sorry if my english isn't well...


MTI Kevin Alquicira Hernández


Programa de Genómica Computacional

Centro de Ciencias Genómicas / UNAM

Av. Universidad s/n Col. Chamilpa 62210,

Cuernavaca, Mor. Tel. (01)777-3132063






De: Arek Kasprzyk <[hidden email]>
Enviado: jueves, 9 de marzo de 2017 08:58 a. m.
Para: Kevin Alquicira
Cc: [hidden email]
Asunto: Re: [Ensembl #177537] Re: Problem with server
 
Hi Kevin,

(Moving this discussion back to the BioMart mailing list).

I could not see anything specific in your error log. I decided therefore to repeat exactly your steps and did not run into any problems. Please see below:


Inline images 1
Clicking on the config brings the default query form as expected:

Inline images 2



Finally, executing the query with all attributes checked, seems to work fine too


Inline images 3


I am running my BioMart on MacOS Sierra 10.12.3


a.












On 9 March 2017 at 10:46, Benjamin Moore via RT <[hidden email]> wrote:
Dear Kevin,

I believe your question is better directed to the BioMart community. It seems
that Arek has helped you on the BioMart mailing list. I'm only really able to
help with problems relating to the Ensembl BioMart. I will now close this
ticket from the Ensembl Helpdesk. Please also remove [hidden email] in
any future replies so that our e-mail system isn't confused!

Best wishes

Ben
Ensembl Helpdesk

On Wed Mar 08 18:53:10 2017, [hidden email] wrote:

  Dear all

  Thanks for the feedback.

  I add the steps with images and the log to know if I am having an error
  when running the server and to be able to receive help.

  Yours sincerely.


   


   

  MTI Kevin Alquicira Hernández

  Programa de Genómica Computacional

  Centro de Ciencias Genómicas / UNAM

  Av. Universidad s/n Col. Chamilpa 62210,

  Cuernavaca, Mor. Tel. (01)777-3132063

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

  De: Arek Kasprzyk <[hidden email]>
  Enviado: martes, 7 de marzo de 2017 02:35 a. m.
  Para: Kevin Alquicira
  Cc: [hidden email]
  Asunto: Re: Problem with server Hi Kevin, I must have missed your initial
  email somehow. I have replied just now to your email on the BioMart mailing
  list. a. On 7 March 2017 at 02:44, Kevin Alquicira <
  [hidden email] (mailto:[hidden email])> wrote:

    Hi

    Please can you help me (It is very important to me)?

    I get the following error when I run the server...

    I followed the manual instructions (http://www.biomart.org/other/biomart_0.9_0_documentation.pdf):

     [1]BioMart 0.9.0 User Manual[2]www.biomart.org10 You will be prompted
    to save the registry file you’ve created, and after doing so the
    server will be deployed on your local machine, port 9000.



    1. http://www.biomart.org/other/biomart_0.9_0_documentation.pdf
    2. http://www.biomart.org

    - Page 9
    To test the registry you can now click on the Start Server button in
    the upper-right...

    I use os x el capitan.

    Sorry but I have no response in the forum.

    https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM

     [1][IMAGE]                                                               [1]An error has occurred on the server...?[2]groups.google.comPosted
                                                                             24/02/17 03:03


    1. https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM
                                                                             1. https://groups.google.com/forum/#!topic/biomart-users/SIiXhDBGTOM
                                                                             2. http://groups.google.com

    Thank you very much


     


     

    MTI Kevin Alquicira Hernández

    Programa de Genómica Computacional

    Centro de Ciencias Genómicas / UNAM

    Av. Universidad s/n Col. Chamilpa 62210,

    Cuernavaca, Mor. Tel. (01)777-3132063




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