[ensembl-dev] Ensembl VM possible to use for house Ensembl installation?
Matthew Laird
lairdm at ebi.ac.uk
Thu Jun 9 09:25:59 BST 2016
Hello Mingyi,
No, I said the VM could be used to point at your own local mirror once
installed. An Ensembl mirror really is no more than a MySQL database
populated with one of our release dumps for one or more species. The
magic sauce is in the API which simply needs to be pointed at whichever
public or private Ensembl database mirror you wish.
The Ensembl Web Code is a bit more of an advanced topic, there are
instructions for installing the Ensembl web code at
http://www.ensembl.org/info/docs/webcode/index.html
On 08/06/16 21:34, Liu, Mingyi wrote:
>
> 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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--
Matthew Laird - Ensembl Core Developer
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-494274
Fax: +44-(0)1223-494468
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