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CHANGELOG.md

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Changelog

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

The format is based on Keep a Changelog.

1.90

Updated

  • RepeatModeler: 2.0.5 -> 2.0.6
  • RepeatScout: 1.0.6 -> 1.0.7

1.89.1

Updated

  • RepeatMasker: 4.1.7 -> 4.1.7-p1

1.89

Updated

  • RepeatMasker: 4.1.6 -> 4.1.7
  • NINJA: 0.99-cluster_only -> 1.00-cluster_only

1.88.5

Updated

  • HMMER: 3.3.2 -> 3.4
  • NINJA: 0.97-cluster_only -> 0.99-cluster_only

1.88 - 2023-12/11

Updated

  • RepeatMasker: 4.1.5 -> 4.1.6

1.87 - 2023-10/17

Updated

  • genometools: 1.6.0 -> 1.6.4
  • coseg: 0.2.2 -> 0.2.3

1.86 - 2023-10/09

Updated

  • RMBlast: 2.14.0 -> 2.14.1
  • RepeatModeler: 2.0.4 -> 2.0.5

1.85 - 2023-5/09

Updated

  • RMBlast: 2.13.0 -> 2.14.0

1.8 - 2023-3/23

Updated

  • RepeatMasker: 4.1.4 -> 4.1.5

1.7 - 2022-11/29

Updated

  • RepeatMasker: 4.1.3-p1 -> 4.1.4
  • RepeatModeler: 2.0.3 -> 2.0.4
  • RMBlast: 2.11.0 -> 2.13.0

1.6 - 2022-10-18

Updated

  • RepeatMasker: 4.1.2-p1 -> 4.1.3-p1

1.5 - 2022-02-09

Updated

  • RepeatModeler: 2.0.2a -> 2.0.3

Changed

  • Updated and expanded upon several sections of the README

1.4 - 2021-05-03

Added

  • Installed ps in the container, for compatibility with Nextflow tracing/metrics

Updated

  • RepeatModeler: 2.0.1 -> 2.0.2
  • UCSC utilities: v407 -> v413

1.3.1 - 2021-04-01

Updated

  • RepeatMasker: 4.1.2 -> 4.1.2-p1

1.3 - 2021-03-23

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
  • RepeatMasker: 4.1.1 -> 4.1.2
  • RMBlast: 2.10.0 -> 2.11.0
    • Upstream BLAST+ 2.11.0 introduced opt-out reporting of usage statistics, which is also included in RMBlast 2.11.0. See http://www.repeatmasker.org/RMBlast.html for more details. To opt out of this, set the environment variable BLAST_USAGE_REPORT=false (e.g. with the -e option to docker run, or the --env option for singularity exec)

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.