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ScriptDocumentation  
Updated Aug 17, 2011 by dez...@gmail.com

Note: some of these scripts warn about invalidating blast-enzyme cache. If you have run one of those commands, be sure to run the rebuild-cache command. Symptoms of a forgotten rebuild-cache include getting no results from enzyme searches at all.

Geovision utility scripts

Data importing

'Actual' data

  • import-sample /path/to/sample.fasta
  • Import a sample file in fasta format. The name of the sample is simply the filename minus the extension.
  • import-database /path/to/database.fasta databasename
  • Import a database file in fasta format. The name of the database is the second command line argument.
  • import-blast /path/to/blast/samplename.databasename.align
  • Import a blast file. The blast file must be named samplename.databasename.align. You must import the database and the sample before all the blasts. If the blast is related to the UniProt database, invalidates the blast-enzyme cache.

Utility databases

  • import-kegg /path/to/kegg/enzyme
  • (Re)import the KEGG enzyme database.
  • import-uniprotecs /path/to/uniprot_sprot.ecs
  • Reimport the UniProt ECS database. Invalidates the blast-enzyme cache.

Service maintenance

  • start-lighttpd, stop-lighttpd
  • Start/stop the Geovision lighttpd HTTP server. The default lighttpd configuration is in $HOME/geovision-lighttpd/ and listens on port 25892.
  • start-localpostgres, stop-localpostgres
  • Start/stop the local Geovision PostgreSQL instance. By default the configuration and data files are located in $HOME/geovision-postgres and listens on port 4394.

Installation

  • install-deps
  • Install all the library dependencies for Geovision.
  • setup-lighttpd
  • Set up a local lighttpd configuration for Geovision. See above for configuration defaults.
  • setup-localpostgres
  • Set up a local PostgreSQL configuration for Geovision. See above for configuration defaults.
  • initial-import
  • Perform the initial database creation & importation. See the installation manual for defaults.

Utilities

  • run-psql args
  • Run psql (the PostgreSQL command line client utility) with the same connection parameters as specified in dbconfig.py
  • create-superuser
  • Create a superuser account. Superusers can log in to the admin panel (http://server/admin/)
  • rebuild-cache
  • Rebuild the blast-enzyme cache and analyze the tables. Run this after all data importing sessions if you have done anything that invalidates the blast-enzyme cache.
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