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Databases-on-SAGA

End user documentation

The following documentation is only applicable to the blast, BUSCO and Kraken2 databases.

  • The databases are updated every 3 months
  • We will keep two previous database versions in case you need them for anything
  • The path to the latest version of each database is /cluster/shared/databases/databaseName/latest
    • In other words, if you want the path to the blast database, substitute databaseName in the path for blast
    • If you want an older version you need to run e.g ls -lh /cluster/shared/databases/blast and check which versions are available

Developer documentation

Basic usage

Assuming that everything has been setup as described below, the basic operation for manual use is ./db-update.sh blast to update the blast database, substitute blast for busco or kraken2 to update them.

Basic setup of the database updating script

N.B these instructions assume that Databases-on-SAGA has been installed on /cluster/shared/databases/admin/.

Preparatory setup

This repository is automatically cloned to /cluster/shared/databases/admin/ by the ansible play (that as of the publication of this update is not been merged yet) in https://gitlab.sigma2.no/sigma2-ansible/sigma-ansible/roles/db-updater/tasks
Assuming that the ansible play is in place, these are the manual steps involved for everything to work properly.

  1. cd /cluster/shared/databases/admin/Databases-on-SAGA
  2. cp -r blast Kraken2 BUSCO /cluster/shared/databases/
  3. Setting up Kraken2
    • cd /cluster/shared/databases/Kraken2/
    • git clone https://github.com/DerrickWood/kraken2/
    • cd kraken2
    • ./install_kraken2.sh /cluster/shared/databases/Kraken2/kraken2/

The ansible play also creates the cron jobs to update the databases and to run the prune-databases.sh script.

Hardcoded paths

The db-updater.sh script has a couple of hardcoded paths that don't need to be changed as long as the instructions above are followed.
But here's a description of the paths in case they do need to be changed:

  1. The mkdest function will create a directory in /cluster/shared/databases/databaseName/todaysDate, each new database is downloaded to this directory
  2. The symlinkDB function makes a fresh symlink of the new database to latest in the /cluster/shared/databases/databaseName/ directory
  3. The kraken2Update function is dependent on the kraken2 git repository having been cloned to and compiled in the /cluster/shared/databases/Kraken2/ directory

Database pruning script

Since no more than two old versions of each database should exist, and the databases get updated every 3 months, the prune-databases.sh script will take care of deleting old databases when there are more than 3 databases and one is older than 3 months
The cron job for it is created by the ansible play linked to above.

Please open an issue if you have any questions.