GitLab

Current version: 3.0.0-beta14

You can check the version installed by running obi --version

Release notes:

• 3.0.0-beta14:

  • Fixed a memory bug when importing a taxdump and building the list of merged taxids
  • Improved disk space management when filling columns

• 3.0.0-beta13:

  • obi import: fixed a critical bug where the last entry of embl and genbank files was not imported.

  • ecopcr now prints a warning instead of stopping when not finding a taxid.

  • Various other small bug fixes, and improvements in documentation, error messages and checks.

• 3.0.0-beta11: Fixed a bug in obi cat when concatenating views with columns having different key sets, and a bug in obi ecotag generating badly formatted column comments.

• 3.0.0-beta10: obi import: new option --preread to do a first readthrough of the dataset if it contains huge dictionaries for a much faster import.

• 3.0.0-beta9: Better disk space management when importing files (rewritten columns are deleted).

• 3.0.0-beta8: Fixed a bug when importing a file where the first entry would contain a dictionary with a single key.

• 3.0.0-beta7: Added the 'obi' prefix in the bash history commands, and fixed a compilation issue with some versions of gcc.

• 3.0.0-beta6: New command: obi cat to concatenate views, and various inconsequential fixes.

• 3.0.0-beta5: Fixed a bug in ngsfilter when there is only one tag.

• 3.0.0-beta4: Fixed and improved the options to keep nucleotides around the amplicon in ecopcr.

• 3.0.0-beta3: Fixed bugs in ngsfilter when cutting sequences, and a few minor bugs.

How to update with git:

From the OBITools3 installation directory and virtual environment, run:

git pull
python3 setup.py install