View on GitHub

This release utilizes the v.2024-04-11 release of the underlying MOAlmanac database and primarily focuses on adding logging to MOAlmanac and refactoring the codebase to remove the datasources/ directory from the application folder. It incorporates changes from two pull requests: https://github.com/vanallenlab/moalmanac/pull/21 and https://github.com/vanallenlab/moalmanac/pull/22.

Additions:

  • A new output with the suffix .log is generated which details inputs provided, configuration settings, output locations, and MOAlmanac processes as they happen. This is detailed in pull request 22.
  • Two new configuration files: annotation-databases.ini and preclinical-databases.ini have been added to the application folder to detail datasource locations for both required datasources and datasources for the cancer cell line modules, respectively. These sections have been removed from config.ini. annotation-databases.ini and config.ini are now required arguments of moalmanac/moalmanac.py and preclinical-databases.ini is an optional argument.

Revisions:

  • The datasources folder, moalmanac/datasources/, was moved to the root directory of this repository.
  • Input, output, and runtime README files have been updated to reflect the changes of these two pull requests.
  • run_example.py was revised to add the date in ISO format to the default output directory
  • Several unit tests were updated to accommodate the datasources location and aforementioned changes to configuration files.
  • The files moalmanac/run_deconstructSigs.R and moalmanac/wrapper_deconstructSigs.sh have been removed from the repository.