[ensembl-dev] MySql database setting and configuration.

Sage Hornung sage.hornung at neogenomics.com
Tue Sep 8 01:19:51 BST 2020

I have asked a few questions recently about setting up an ensemble rest and an ensemble database. I appreciate the all the help.

I was able to get all the Ensembl data imported after a couple weeks but unfortunately its already corrupted one or more of my InnoDB tables.

I previously asked I am not opposed to using the cached data and I ended up adding it but one of the rest endpoints supposedly ignores and bypasses the cache. This one in particular https://grch37.rest.ensembl.org/vep/human/hgvs. We are only using a few endpoints and the whole point of this was to speed some of these requests up for ourselves.

Our MySQL database server has 14GB ram and 4 cores and 2TB of storage. I followed the directions on the Ensembl website for importing the data but the only way I was able to get the larger tables to import was changing the storage engine to InnoDB. Im not sure if this was the best choice because its seems the MyISAM engine is better for read data. But this is the only way I was able to get it to successfully  import the data.

I guess my question is was this a good idea? Is there any specific settings I should be using when configuring MySQL? I have used a few tools online and most say my settings are good/ok doe my configuration. The homo_sapiens_variation_100_37 is the only one that's giving me issues and only with the tables greater than 25GB. Some of these tables are massive I am looking for any tips or suggestions when dealing with them.

Thank You,
Sage Hornung

Sage Hornung
Software Engineer
NeoGenomics Laboratories, Inc.
2131 Faraday Avenue, Carlsbad, CA 92008
Phone: 760.516.5114
Cell: 760.755.3930
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