[ensembl-dev] Ensembl Mirror Install - BioMart Installation

Thu Jan 18 15:49:09 GMT 2018

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
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>>
>>
>>
>
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DBI connect('database=ensembl_archive_91;host=localhost;port=3306','root',...) failed: Unknown database 'ensembl_archive_91' at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/DBSQL/Archiv
DBI connect('database=ensembl_production_91;host=localhost;port=3306','root',...) failed: Unknown database 'ensembl_production_91' at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/DBSQL/
REQUEST(G): [served at Thu Jan 18 14:09:24 2018 by 29791 in 37ms] /index.html
[Thu Jan 18 14:09:25 2018] Child initialised: 29801
[Thu Jan 18 14:09:26 2018] Child initialised: 29802
[Thu Jan 18 14:09:26 2018] Child initialised: 29803
[Thu Jan 18 14:09:27 2018] Child initialised: 29812
[Thu Jan 18 14:09:27 2018] Child initialised: 29813
[Thu Jan 18 14:09:27 2018] Child initialised: 29814
[Thu Jan 18 14:09:27 2018] Child initialised: 29815
Use of uninitialized value in sprintf at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Controller/Psychic.pm line 274.
Use of uninitialized value $site in concatenation (.) or string at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Controller/Psychic.pm line 239.
ORMException Exception:
  Module 'ORM::EnsEMBL::DB::Session::Object::Session' could not be loaded: Attempt to reload ORM/EnsEMBL/DB/Session/Object/Session.pm aborted.
Compilation failed in require at (eval 3870) line 2.
  Thrown by EnsEMBL::Web::Controller::process in module EnsEMBL::Web::Apache::SpeciesHandler at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm on line 102
  Called by EnsEMBL::Web::Apache::SpeciesHandler::handler in module EnsEMBL::Web::Apache::Handlers at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Apache/Handlers.pm on line 470
  Called by EnsEMBL::Web::Apache::Handlers::handler in module main at -e on line 0
  Called by (eval) in module main at -e on line 0 at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Exception.pm line 70.
ERROR: be019ffe39 (/Multi/Search/Results?species=all;idx=;q=BRCA2;) (Server Exception)
Uncaught exception 'ORMException' with message 'Module 'ORM::EnsEMBL::DB::Session::Object::Session' could not be loaded: Attempt to reload ORM/EnsEMBL/DB/Session/Object/Session.pm aborted.
Compilation failed in require at (eval 3870) line 2.
'
  Thrown by EnsEMBL::Web::Controller::process in module EnsEMBL::Web::Apache::SpeciesHandler at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm on line 102
  Called by EnsEMBL::Web::Apache::SpeciesHandler::handler in module EnsEMBL::Web::Apache::Handlers at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Apache/Handlers.pm on line 470
  Called by EnsEMBL::Web::Apache::Handlers::handler in module main at -e on line 0
  Called by (eval) in module main at -e on line 0 at /home/ensembl/local/ensembl_91/ensembl-webcode/modules/EnsEMBL/Web/Apache/ServerError.pm line 72.
REQUEST(G): [served at Thu Jan 18 14:09:31 2018 by 29791 in 26ms] /Multi/Search/Results?species=all;idx=;q=BRCA2;
[Thu Jan 18 14:09:53 2018] Child exited: 29812
[Thu Jan 18 14:09:53 2018] Child exited: 29815
[Thu Jan 18 14:09:53 2018] Child exited: 29803
[Thu Jan 18 14:09:53 2018] Child exited: 29813
[Thu Jan 18 14:09:53 2018] Child exited: 29800
[Thu Jan 18 14:09:53 2018] Child exited: 29814
[Thu Jan 18 14:09:53 2018] Child exited: 29797
[Thu Jan 18 14:09:53 2018] Child exited: 29799
[Thu Jan 18 14:09:53 2018] Child exited: 29796
[Thu Jan 18 14:09:53 2018] Child exited: 29801
[Thu Jan 18 14:09:53 2018] Child exited: 29792
[Thu Jan 18 14:09:53 2018] Child exited: 29802
[Thu Jan 18 14:09:53 2018] Child exited: 29791
[Thu Jan 18 14:09:53 2018] Child exited: 29798
[Thu Jan 18 14:09:53 2018] Child exited: 29794
[Thu Jan 18 14:09:53 2018] Child exited: 29793
[Thu Jan 18 14:09:53 2018] Child exited: 29795
[Thu Jan 18 14:09:53 2018] [notice] caught SIGTERM, shutting down
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