Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.1.0] - 2023-3-1

Added

Support to upgrade and uninstall EukMetaSanity from INSTALL.sh script

Changed

Installation script now fails on error (as expected)
The bin/ directory is no longer version-controlled
- Will auto-generate as part of installation process
Update to YAPIM v0.3.2
If available, augustus uses GeneMark-derived proteins for first-pass predictions
- Otherwise, performs legacy taxonomy search and uses closest augustus species for first-pass

Fixed

The report pipeline failed to annotate results of refine pipeline
Parsing existing pipeline results failed on non-uniform recorded result directories
Transcriptome-related Tasks defined implementations for incorrect versions of GMAP
BRAKER2 now populates expected output
Taxonomy parsing algorithm was incorrect
Redundant MMSeqs databases were created
Reduce temporary file retention

Removed

Ability to set database directory as part of installation
Ability to skip database downloads as part of installation
Ability to skip RepeatMasker database downloads as part of installation

[1.0.0] - 2021-07-25

First release of EukMetaSanity