Definitions
  • Bank: Any file or set of files located on a remote server
  • Process: All transformations applied
    upstream or downstream of the bank download
    (scripts)

BioMAJ needs to know three parameters to get a new bank:

  • configuration parameters with the global.properties file
  • which database to update with the bank.properties files
  • which processes (alignment, indexation …) will be applied to the database with the process files

Workflow

The BioMAJ workflows takes place as follows, the pre-processes are the first to be applied (get files from a private bank, checking disk space, etc.). Then the workflow checks the release information, if there is already the same release in the database, the workflow stops. If there is a new release, the bank files are downloaded and uncompressed in the offline-dir directory. It is possible to choose which files to keep in the in the bank’s final directory. The workflow applies post-processes, and delete old version of the bank (if necessary). At the end of the workflow the bank will be published, which creates a current symlink.

See how the different architectures work here.