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@vinuesa vinuesa released this 21 Nov 17:40
· 170 commits to master since this release
v2.0.0
91df9bc

GET_PHYLOMARKERS_v2.0.0_2022-11-20

This release (2022-11-20) contains new features, significant code improvements, binary updates, and some bug fixes

New features

The most salient new feature is that run_get_phylomarkers_pipeline.sh now also calls ASTRAL-III to estimate a concatenation-independent species tree, using as input the filtered gene trees estimated by iqtree2 from the core-genome clusters computed by get_homologues.

IQTree2 calls have been updated to match those of version 2.2.0 and replaced the -T AUTO with the -T $IQT_threads call, which results in a ~20-fold speedup when running the included run_test_suite.sh.

The main scripts run_get_phylomarkers_pipeline.sh and estimate_pangenome_phylogenies.sh have been thoroughly revised, fixing bugs, using a more idiomatic and modern bash syntax, and improving code layout for better legibility. Both scripts require bash v4.3 or newer, and the new function check_bash_version ensures that the host runs a proper version.

Updated external programs

Updated scripts and library code

  • run_get_phylomarkers_pipeline.sh
  • estimate_pangenome_phylogenies.sh
  • run_kdetrees.R
  • lib/get_phylomarkers_fun_lib

New scripts

install_kdetrees_from_github.R

Docker image

The distribution contains a Dockerfile used to build the Docker image ready to pull from Docker Hub.

Documentation

  • Updated documentation and tutorial materials, both in Markdown and HTML formats

Travis CI and updated test suite

  • CI with 23 tests implemented in test_get_phylomarkers.t, deployed using Travis CI
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