Precompiled Chado Databases
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
- 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:
- Relationship Ontology
- Sequence Ontology
- Gene Ontology
- Chado Feature Properties
- 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.