[ensembl-dev] Ensembl Mirror Install - BioMart Installation

[Matthew Laird]

Hello Fazulur,

I just spoke with our web team who maintains that code and better knows 
how to debug it. They requested you please submit a ticket through our 
helpdesk [1] about this so they can better track the responses and 
assist you with your issues. Thanks.

[1] https://www.ensembl.org/info/about/contact/index.html

On 18/01/18 15:49, Rehaman wrote:
> Dear Matthew,
>
> We have installed Ensembl server as per instructions 
> (https://asia.ensembl.org/info/docs/webcode/mirror/index.html) and 
> able to see ensembl webpage.
>
> Homo sapiens data loaded to MySQL and updated .ini files as 
> instructed. Created species specific ini files (homo_sapiens.ini) and 
> added organism specific databases and restarted the server. When 
> queried for BRCA2 under homo_sapiens it's giving error. We spend some 
> time to debug and not succeeded. Please find attached screen shot of 
> private server and error log.
> Its related to ORM and few perl modules. All dependency modules 
> including "Rose" were installed and exported perl5lib too.
>
> Could you please suggest me how to resolve this.
>
> Thanks in Advance
> Fazulur Rehaman
>
> On Sun, Jan 14, 2018 at 5:47 PM, Rehaman <ensemblfan at gmail.com 
> <mailto:ensemblfan at gmail.com>> wrote:
>
>     Dear Matthew,
>
>     Thanks a lot for your answer.
>
>     We are still in installation process of private ensemble server.
>     We will post if we have any further issues.
>
>     Thanks & Regards
>     Fazulur Rehaman
>
>     On Fri, Jan 12, 2018 at 4:14 PM, Matthew Laird <lairdm at ebi.ac.uk
>     <mailto:lairdm at ebi.ac.uk>> wrote:
>
>         Hi Fazulur,
>
>         I've raised the issue with the appropriate teams that yes we
>         have local installation instructions but we don't have release
>         to release upgrade instructions. To upgrade from one release
>         to the next:
>
>         - download and install the latest database versions of the
>         species you want in your local installation, as per the
>         installation instructions
>         - for each of the ensembl* git repositories, in the directory
>         for that repository run: git fetch; git checkout release/91
>         (where you replace the 91 with whichever new version in the
>         future)
>         - delete everything in the conf/packed directory for the web code
>         - restart the web server, as per the installation instructions
>
>         If you have any trouble with this, please let us know and
>         we'll try to assist you.
>
>         Cheers.
>
>
>         On 11/01/18 06:47, Rehaman wrote:
>>         Dear Ensembl team,
>>
>>         Thanks a lot for quick response.
>>
>>         I have one more question.
>>         Could you please let me know how to update our private server
>>         for next Ensembl's release.
>>
>>         Thanks & Regards
>>         Fazulur Rehaman
>>
>>         Thanks & Regards
>>         Fazulur Rehaman
>>
>>         On Wed, Jan 10, 2018 at 4:40 PM, Matthew Laird
>>         <lairdm at ebi.ac.uk <mailto:lairdm at ebi.ac.uk>> wrote:
>>
>>             Hello Rehaman,
>>
>>             Unfortunately I think you've misunderstood what the
>>             installation instructions are trying to say. We no longer
>>             recommend the local installation of BioMart as part of a
>>             local mirror, and when the documentation says to link to
>>             a public BioMart, it means to run your queries against a
>>             public BioMart and Ensembl database. There isn't a way to
>>             have our public BioMart instances talk to your private
>>             server. If you need to do large queries against a local
>>             Ensembl mirror, you're better off using the API in that case.
>>
>>             Please let us know if you have any further questions.
>>             Cheers.
>>
>>
>>             On 10/01/18 10:46, Rehaman wrote:
>>>             Dear Team,
>>>
>>>             We are configuring Ensembl mirror locally in our
>>>             environment as per instructions.
>>>             Now we need to install BioMart. In Documentation, It is
>>>             saying that it is not recommended to install.
>>>
>>>             Could you please let us know the process of
>>>             linking public BioMart.to ensembl local server?
>>>
>>>             Thanks in advance
>>>             Rehaman
>>>
>>>
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>>
>>
>
>
>

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