How Do I Do A Local Build Of Ensembl'S Mysql Database?
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13.2 years ago
Blunders ★ 1.1k

Is this the best how to guide on doing a full local mirror of the Ensembl's MySQL database?


Very possible that I'm wrong, but based on a quick review there appears to be typos in the how to, for example:

create database homo_sapiens_core_61_37f

Should be:

create database homo_sapiens_core_61_37f;

note that the ";" or semi-colon is missing at the end.

While is is not a major issue, just making sure I'm looking at the best and most up to data guide to doing this.


Questions, feedback, requests -- just comment, thanks!!

ensembl mysql • 3.4k views
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13.2 years ago
User 6659 ▴ 980

This is the guide i used. I'm not sure it can be any more up-to-date though - there are only 3 sql statements you need to import the database (though you can do it differently if you want to speed things up)

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13.2 years ago
Darked89 4.6k

While ENSEMBL guide is way more recent there are more comprehensive (but by no means complete or finished) descriptions how to get the local installation up and running:

http://openwetware.org/wiki/Wikiomics:Ensembl_local_install

and

http://openwetware.org/wiki/Wikiomics:Ensembl_local_install_draft

In a some free moment I hope to update it to the current versions of ENSEMBL, Perl etc. but do not count on this happening in the next few weeks.

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@darked89: Super, thanks for sharing -- all and all, I just looking for semi-recent guides to rolling out ENSEMBL, so your answer so far is the best. Selecting you as the answer for now. Again, thank you!!

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Entering edit mode
13.2 years ago

This is an up-to-date guide, however, we should do a careful reread for typos. Thank you for pointing this out to us.

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@Giulietta - Ensembl Helpdesk: Appears that's not a typo in the SQL, I'd double check with someone that "really" knows SQL. Cheers!

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Our webteam agrees about the semicolon- it has been added in, so you'll see it on the next release. They are MySQL masters, don't worry. =) The rest of the doc looks fine to them.

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