Precompiled Chado Databases

Revision as of 17:41, 5 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, as all you need to do is change the username in the precompiled schema

  sed -i "s/schema_builder/user_name/g" csb.sql

and load it into the database of your choice.

  psql -U {user_name} -d {desintation_db} -f csb.sql

This process takes ~10 seconds, compared to the 1.3 hours (according to my jenkins job) for regular ontology loading.

The databases can be found here: [ ]

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.