Skip to content

Latest commit

 

History

History
104 lines (71 loc) · 3.27 KB

CHANGELOG.md

File metadata and controls

104 lines (71 loc) · 3.27 KB
Raw

Changelog

1.3.0 (2022-03-01)

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

1.2.0.2 (2021-11-15) - pypi release only

Bugfixes

  • Update python requirements

1.2.0.1 (2018-09-25) - pypi release only

Bugfix release

1.2.0 (2018-07-17)

Major changes

  • Dot plot have now a mouse cursor centered zoom
  • Now includes mashmap (v2.0), a faster aligner for high identity genomes, as an alternative to minimap2 (Linux only)
  • Download a HTML page which permit to show an interactive dot plot offline (with the summary)
  • Display match coordinates by moving the mouse cursor over the match line

Other changes

  • Upgrade embedded minimap2 to the latest available version (2.11)
  • Add help messages on the interface
  • Add the ability to add a message to the run form through command line (designed for maintenance for example)
  • Several bug fixes

1.1.1 (2018-06-20)

Bugfixes

  • Fix bug with parse of MAF files
  • Fix incompatibility with pip >= 10.0

1.1.0 (2018-04-17)

Major changes

  • Improve run form: add support for uploading an alignment file (PAF or MAF by default) instead of fasta files, if alignment file is already available
  • Add export of a job into a backup, which can be re-uploaded with the run form
  • Ease the integration of new tools or new file formats
  • Allow to install as simple user on Unix systems

Other changes

  • Export of the dot plot is now done including the zoom factor
  • Add new color palettes for dot plot
  • Add analytics logs (anonymous) which permits to know which size of genomes are ploted (can be disabled)
  • Improve documentation
  • Minor bug fixes

1.0.1 (2018-02-23)

Bug fix release.

Changes

  • Fix bugs
  • Disable export of fasta files for gallery items

1.0.0 (2018-02-21)

First stable release