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Implement new generation database

  • MySQL server runnign on Mammoth
  • simple file-based database for testing

MySQL

Erik Storrs: okay so got a start on the documentation and there is now a cromwell server and database running on mammoth. Barebones documentation for setting up or restarting the server is here https://github.com/estorrs/cromwell-server

Cromwell version

Erik currently using Cromwell v78 running on

http://mammoth.wusm.wustl.edu:3307

File-based database

Work by MAW described here: /cache1/fs1/home1/Active/home/m.wyczalkowski/Projects/CWL-dev/SomaticSV-dev/SomaticSV.database/README.database.md

FileDB is a good solution for one-off runs, like those in CWL testing scripts (cromwell-simple). For production runs recommend MySQL

Background reading

https://cromwell.readthedocs.io/en/stable/Configuring/ (Cromwell server on MySQL Database)

https://docs.docker.com/compose/