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CHANGELOG.md

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Changelog

1.5.0 (2023-05-04)

Changes

If you run dgenies in webserver mode, database schema has changed.

The column batch_type was changed to runner_type in job table. You can update the database with following sql command:

ALTER TABLE job RENAME COLUMN batch_type TO runner_type;

This change was also reflected for cluster configuration in application.properties, where batch_system_type was renamed to runner_type.

For users:

  • Update batch mode:
    • Local files upload
    • Batch content checked in web interface
    • Single upload per file
    • Batch file format has changed, in particular, option keys have been change to be more comprehensible. Please read the doc.
  • Dotplot:
    • Files generated through "Query Fasta" and "Query assembled as reference" are updated if new sorting and contig reversal are done.
    • Files linked in email are stable until the job is cleanned. They dont change if sort and contig reversal are updated.
    • You can reset the sort (usefull when playing with manual contig reversal)
    • "Query assembled as reference" file is now compressed in webserver mode.
  • Job logs are now available to download and are included in backup file.
  • Update user interface to bootstrap 4.6

For sysadmin:

  • Tools config file format (tools.yaml) has changed. Please update it if you use a custom one.
  • Basic app logging.
  • Configuration files:
    • In application.properties, batch_system_type was renamed to runner_type in order to avoid confusion with batch jobs intoduced with dgenies 1.4.
    • Cluster walltime can be set in the config file.
    • In database, the column batch_type was changed to runner_type in job table.
    • It is possible to set config files directly when running dgenies with --config and --tools-config options. Please be careful to use the correct config files when managing a running instance of dgenies.
    • It is now possible to use a the option --flask-config in order to set some flask options. You can use it to set some email server parameters.
    • For server mode, the number of download sessions in parallel can be now set with max_download_sessions (default is alway 5). Session delays can also be modified now.
    • Reinforce tar file checking
    • Drop Flask<2

Bugfix

  • When sorted, "Association table", "Query Fasta" and "Query assembled as reference" files match dotplot. Before, only the last reversed contig on dotplot was token in account.
  • Fix some bugs with Flask>=2
    • Add compatibility with Flask 2.2
    • Some gzipped files were uncompressed by browser when downloaded.
    • Backup file name was incomplete.

1.4.0 (2022-07-12)

Major change

  • Add batch mode. This early version only allows to use urls as file inputs. #28

Minor changes

  • Add definition page to explain how some things like Identity, Best matching chromosomes are computed.
  • Relax Jinja and Flask requirements up to last versions

Bugfix

  • Some options were display to right side of page

1.3.1 (2022-03-30)

Minor change

  • Add some anonymization strategies

Bugfix

  • Fix some Jinja2 requirement constraints
  • Fix exported query fasta file that was not compressed when asked.

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