D-Genies 1.3.0

Major changes

• Add repeatedness option with minimap2. This option needs to upgrade the database schema with following command:

  ALTER TABLE job ADD COLUMN options VARCHAR(127) NULL;

• Backup archive is now a tar.gz file. Old tar backup archive are still supported
• Upgrade embedded minimap2 to the latest available version (2.24)
• GDPR compliant (webserver mode):
  • Cookie wall option
  • Ability to set legal stuff pages
  • Analytics is now anonymous, an option allows to restore the previous behavior

Other changes

• Python 3.10 compatibility
• Add a command to clean analytics DB from dgenies (dgenies clear -a [--max-age <age>])
• Check if PAF file is correctly formatted
• Performance improvement
• Expose max_nb_lines parameter in configuration file.
• Tools can have a label now (in tools.yaml).
• Speedup compressed file operations by using xopen library
• Fix upload form. Form is now correctly reset when a field is missing or erroneous.
• Fix filename collision. Uploading a query file and a target file with the same filename now works correctly
• Fix wrong RAM usage displayed in gallery
• Correct default slurm parameters to match last version of slurm-drmaa (1.1.3)
• Remove local scheduler pid file when stopping it
• Update documentation:
  • Explain how similarity/identity measure is computed
  • Add link in D-Genies to what is expected in backup archive
• Wiki
  • Cookbooks
  • Additional information for developers