[BioMart Users] Help with Installation

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[BioMart Users] Help with Installation

Sri Krishna Suresh Kumar
Hello,

I am trying to install Biomart on a Ubuntu based system. I have
installed Apache, Mod_Perl and When I trying to configure MartView
with the registryURL file(attached), I am getting error (Attached).

I am not sure where the error is. Could you help me pointing out where
the error is?

Thanks and regards,
Sri Krishna

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Error.log (3K) Download Attachment
registryURLPointer.xml (480 bytes) Download Attachment
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Re: [BioMart Users] Help with Installation

Elena Rivkin
Sri Krishna,

Did you check all the possible reasons indicated in the error message?

Thank you,
Elena



On 11-04-29 3:04 PM, "Sri Krishna Suresh Kumar" <[hidden email]>
wrote:

>Hello,
>
>I am trying to install Biomart on a Ubuntu based system. I have
>installed Apache, Mod_Perl and When I trying to configure MartView
>with the registryURL file(attached), I am getting error (Attached).
>
>I am not sure where the error is. Could you help me pointing out where
>the error is?
>
>Thanks and regards,
>Sri Krishna

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Re: [BioMart Users] Help with Installation

Sri Krishna Suresh Kumar
Hello Elena,

I did check if I had XML::Simple Installed. It has been installed to
the latest version.
The params in the registryURL file is to a demo site, which is
supplied along with the installation. Hence, I am not sure where the
problem is.

Regards,
Sri Krishna

On Fri, Apr 29, 2011 at 9:35 PM, Elena Rivkin <[hidden email]> wrote:

> Sri Krishna,
>
> Did you check all the possible reasons indicated in the error message?
>
> Thank you,
> Elena
>
>
>
> On 11-04-29 3:04 PM, "Sri Krishna Suresh Kumar" <[hidden email]>
> wrote:
>
>>Hello,
>>
>>I am trying to install Biomart on a Ubuntu based system. I have
>>installed Apache, Mod_Perl and When I trying to configure MartView
>>with the registryURL file(attached), I am getting error (Attached).
>>
>>I am not sure where the error is. Could you help me pointing out where
>>the error is?
>>
>>Thanks and regards,
>>Sri Krishna
>
>
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Re: [BioMart Users] Help with Installation

Joachim Baran-2
Hi Sri!

  Can you give me a short run through what you are trying to achieve?

  The conf-file you used does indeed not work with our central portal
anymore, because it has grown considerably since the documentation was
written. It comes with all kinds of configurations now. I still works on
"www.ensembl.org". If you really want to replicate our central portal,
then we can send you the XML-files for that instead.

  If you try to set up a new mart from scratch, it might be easier to use
the all new BioMart 0.8 version instead. It is easier to use and is in
active development. Have a look at its documentation:
http://www.biomart.org/rc5_documentation.pdf

Joachim

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Re: [BioMart Users] Help with Installation

Joachim Baran-2
Hi, again!

  As a follow up: the problem with registryURLPointer.xml seems to affect
only certain marts.

  Please try other values for "msd,uniprot". For example, "ensembl" seems
to work.

  A full list of available marts can be found here (see the "name"
attribute for possible mart-names):
http://www.biomart.org/biomart/martservice?type=registry

Joachim

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