Precompiled Chado Databases

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Revision as of 19:22, 13 February 2014 by Eric Rasche (Talk | contribs)

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I'm not aware of how many of you regularly have to configure and deploy chado databases, however over time I've found that a significant portion of my time was spent waiting on ontologies to load.

To this end (and in support of some other projects), I set up a jenkins job to

  • clone chado from SVN
  • build
  • load ontologies
  • dump database as sql
  • upload to a publicly accessible webserver

This is done on a weekly basis. I'm making the compiled databases with all 5 ontologies loaded available to the community. They're trivial to use if you're just trying to install chado. This process takes ~10s-5m, compared to the 1.3 hours (according to my jenkins job) for regular ontology loading.

The databases can be found here: [https://cpt.tamu.edu/~docs/chado/ ]

The ontologies currently installed are:

  1. Relationship Ontology
  2. Sequence Ontology
  3. Gene Ontology
  4. Chado Feature Properties
  5. Plant Ontology

If anyone is interested in this, and would like:

  • other builds with different (sub)sets of
  • archived copies of schemas over time

please feel free to [request] them and we'll add them to the jenkins job/make them available.

NB: The caveats of this method are, of course, that none of the scripts are installed, and the gmod conf files are not created in GMOD_ROOT. However, for remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this seems to be fine.