CHANGELOG.md

Changelog

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

The format is based on Keep a Changelog.

1.3-beta-1 - 2021-01-15

Added

• Installed strace in the container
• Added several of the UCSC utilities (faToTwoBit, twoBitInfo, twoBitToFa). These tools are used by some of the scripts in RepeatModeler/util.

Updated

• HMMER: 3.3 -> 3.3.2
• RepeatModeler: 2.0.1 -> 2.0.2-beta-4

Fixed

• coseg: set a working path to a perl interpreter in .pl scripts

1.2 - 2020-09-09

Added

• TRF: 4.09.1

Updated

• LTR_retriever: 2.8 -> 2.9.0
• MAFFT: 7.453 -> 7.471
• RepeatMasker: 4.1.0 -> 4.1.1

Changed

• dfam-tetools.sh: --trf_prgm is no longer necessary and is ignored

Fixed

• dfam-tetools.sh: Fix compatibility with macOS (fixes #3)
• dfam-tetools.sh: Use the '--init' option when running docker to avoid a zombie apocalypse (fixes #2)

1.1 - 2020-01-13

Updated

• LTR_retriever: 2.7 -> 2.8
• genometools: 1.5.10 -> 1.6.0
• HMMER: 3.2.1 -> 3.3
• RepeatModeler: 2.0 -> 2.0.1
• RMBlast: 2.9.0-p2 -> 2.10.0
• MAFFT: 7.429 -> 7.453

Changed

• Use the C locale for singularity when running via dfam-tetools.sh, silencing some warnings from perl programs.

Fixed

• Fixed the HMMER path for RepeatMasker, so that -engine hmmer will work properly.

1.0 - 2019-11-15

Added

• First release.