[ensembl-dev] Ensembl Mirror Install - orm errors
Emily Perry
emily at ebi.ac.uk
Tue Jan 23 11:25:55 GMT 2018
Hi Rehaman
We did not receive a request for you on helpdesk, so I'm not sure what
happened. I have just created a ticket for you, numbered 238614. You
should get a reply to this soon.
All the best
Emily
On 23/01/2018 04:20, Rehaman wrote:
> Dear Matthew,
>
> With respect to my previous question about errors on Ensembl
> installation, I submitted to helpdesk, till now I didn't get any
> response from them. I have given my mail ID (vrehaman at gmail.com
> <mailto:vrehaman at gmail.com>) while submitting to help desk.
>
> Could you please let me know the status and help me to resolve the issue.
>
> Thanks In Advance
> Fazulur Rehaman
>
> On Fri, Jan 19, 2018 at 7:50 AM, Rehaman <ensemblfan at gmail.com
> <mailto:ensemblfan at gmail.com>> wrote:
>
> 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
> <mailto: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
> <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
>> <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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--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
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