[ensembl-dev] Ensembl Mirror Install - BioMart Installation

[Rehaman]

Dear Matthew,

Thanks a lot for your response. I have submitted the same.

Thanks & Regards
Fazulur Rehaman

On Thu, Jan 18, 2018 at 9:27 PM, Matthew Laird <lairdm at ebi.ac.uk> wrote:

> 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> 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> 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> 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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