Thanks to everyone for their input.
John, your explanation was excellent. I completely agree with the implementation of galaxy as it stands now (with a minor documentation warning about default
mysql engine switch in v5.5). Personally, I either place trust in the ORM to maintain referential integrity or I offload it to the DB Engine. Hence, I will keep the MyISAM tables going for now after I do some validation against an InnoDB database (please
no MyISAM engine hate-mail LOL).
With respect to dropping MySQL support, I will let that one go by for now LOL.
Thanks again for your contributions and maintenance of this great platform. I feel that it will be a game changer in the bioinformatics community.
Regards,
Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel Iyad.Kandalaft@agr.gc.ca
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada
From: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: Thursday, June 12, 2014 9:16 AM
To: Hans-Rudolf Hotz
Cc: John Chilton; Kandalaft, Iyad; galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy updated botched?
Hey Hans (and anyone else using MySQL),
Just to clarify -- MySQL doesn't have this (particular) error by default and as long as your server default table type has not and does not change you should be fine.
I've just successfully tested MySQL using MyISAM all the way to the current tip revision and you should be able to upgrade safely when the time comes.
-Dannon
On Thu, Jun 12, 2014 at 2:01 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
On 06/12/2014 12:06 AM, John Chilton wrote:
If anyone out there has tired using Galaxy with strictly MyISAM tables
and found it untenable - by all means please chime in.
Well, due to several reasons we are (still) using MySQL (version: 5.1.69) with only MyISAM tables. We have been running into troubles but they were never related to running MyISAM.
However, I haven't done the latest Galaxy code upgrade, hence we are still on database version '118'. So, I am curious to see what will happen when I do the next upgrade (after GCC).
Also, on my list of things to do for this year is actually changing all our Galaxy servers from MySQL to PostgreSQL. With my current workload, I doubt I will manage to do this and have to postpone this 'adventure' to next year.
Regards, Hans-Rudolf
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