[ensembl-dev] Ensembl Mirror Install - BioMart Installation

Matthew Laird lairdm at ebi.ac.uk
Fri Jan 12 13:14:07 GMT 2018

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.


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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