[ensembl-dev] Ensembl VM possible to use for house Ensembl installation?

[Liu, Mingyi]

Hi, Matthew,

Thanks for your reply! So as you said, VM is not for local mirror, which I understood. You also said that VM could be used for local mirror once registry is pointed to the local MySQL instance. This part I'm confused about.

A local mirror for Ensembl should also contain a website that serves up the Ensembl genome browser/search results etc., and allow a local DAS server as needed.  How is that done with the VM? I couldn't find any apache webserver included, or where the usual Ensembl webcode config scripts are located.

Or by a local mirror, you meant the mirror for the Ensembl data (in MySQL), not the mirror for the Ensembl website? The latter is what I want to use VM for but I think it's not possible (would've been nice though!).

Thanks again!

Mingyi

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Matthew Laird
Sent: Wednesday, June 08, 2016 4:22 PM
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] Ensembl VM possible to use for house Ensembl installation?

Hello Mingyi,

Indeed the VM is intended to assist users in rapidly using the API, users who might be running Windows or not want to install the API locally, the VM lets them prototype or rapidly start using the API with minimal effort. As you've discovered it's not intended to be a local Ensembl mirror, it's a client side installation.

Installing a mirror is actually even easier than setting up the API, dumps of all the Ensembl databases are available on our ftp site at ftp://ftp.ensembl.org/pub/current_mysql/ And instructions for loading them in to a local MySQL instance are available at http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html Once that's done, all you need to do is point the Registry at your local instance rather than one of the public mirrors, and voila, you have your own mirror of an Ensembl release.

If you have any other questions don't hesitate to drop us another message.
On 16-06-08 08:33 PM, Liu, Mingyi wrote:
Hi, can anyone confirm my question below? Are the Ensembl VMs only for Ensembl API + Ensembl's own MySQL access, or the VM has everything needed for in-house Ensembl installation (one just need to change some parameters to point to in-house MySQL etc)? If the latter that'd be fantastic, but so far it doesn't look like the case.

Thanks!

Mingyi

From: Liu, Mingyi
Sent: Tuesday, June 07, 2016 1:48 PM
To: Ensembl developers list <dev at ensembl.org><mailto:dev at ensembl.org>
Subject: Ensembl VM possible to use for house Ensembl installation?

Hi,

I downloaded Ensembl VMs in the hope that this is an easy way to set up Ensembl in-house (once MySQL data are all downloaded/imported). However it seems that the VM doesn't have webserver and is only meant to be used for running scripts that utilize Ensembl API?  Is that correct? I'm a bit confused as I thought one doesn't need a VM to run scripts using Ensembl API, just need to download Ensembl/Bioperl and install dependency. So the VM is mostly for saving efforts installing dependency?

Thanks!

Mingyi
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