Dgenies 1.5.0

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;

and if you use analytics

ALTER TABLE analytics 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.

D-Genies 1.4.0

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

D-Genies 1.3.1

Minor change

• Add some anonymization strategies

Bugfix

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

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

D-Genies 1.2.0

Major changes

• Dot plot have now a mouse cursor centered zoom
• Now includes mashmap, 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

How to install?

See instructions here

D-Genies 1.1.1

Changes

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

How to install?

See instructions here

D-Genies 1.1.0

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

How to install?

See instructions here

D-Genies 1.0.1

Bug fix release.

Changes

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

How to install?

See instructions here

D-Genies 1.0.0

First stable release

How to install?

See instructions here