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VEBA_v2.2.0
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@jolespin jolespin released this 10 Jun 01:16
· 46 commits to main since this release
v2.2.0
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Learn about vigilant mode.

Disclaimer:
I made some large updates in this version and I believe everything has been adequately tested but just in case anything has slipped between the cracks you can use v2.1.0 which has been thoroughly tested in accordance to the NAR Espinoza 2024 paper. Benefits of using this version include much faster and robust prokaryotic classifications and fast/scalable HMM-based annotation modeling.

Large performance updates for this version including:

  • Updating GTDB-Tk 2.3.0 -> 2.4.0 which means the GTDB needed to be updated from r214.1 -> r220
  • VEBA-classify_env was split up into VEBA-classify-eukaryotic_env, VEBA-classify-prokaryotic_env, and VEBA-prokaryotic_env
  • annotate.py, classify-eukaryotic.py, and phylogeny.py were rewritten (and their utility scripts) were updated to used PyHMMER (pyhmmsearch and pykofamsearch) which is faster than HMMSearch when multithreaded.
  • KOFAM was changed to KOfam

NOTE: Please don't use the tar.gz as it contains the 2.1.0 version for some reason:

VERSION="2.2.0"
# wget https://github.com/jolespin/veba/archive/refs/tags/v${VERSION}.tar.gz # The .tar.gz is out of date in this release
# tar -xvf v${VERSION}.tar.gz && mv veba-${VERSION} veba

# Alternative download
wget https://github.com/jolespin/veba/releases/download/v${VERSION}/v${VERSION}.zip
unzip -d veba v${VERSION}.zip
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