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GET_PHYLOMARKERS_v2.2.1_2024-04-18

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@vinuesa vinuesa released this 19 Apr 00:06
· 11 commits to master since this release
v2.2.1
805047d

This minor release (v2.2.1, 2024-04-18) contains the following improvements:

  • run_get_phylomarkers_pipeline.sh v2.8.1.4_2024-04-17
    • Improved reporting at the end of run (STDOUT and file written to disk) of essential output files and figures generated by the pipeline, calling new functions rm_top_dir_prefix_from_wkdir and read_svg_figs_into_hash
  • get_phylomarkers_fun_lib v2024-04-17
    • created new functions rm_top_dir_prefix_from_wkdir and read_svg_figs_into_hash
    • prepended missing "$bindir"/ to several iqtree calls in run_ASTRAL and compute_ASTRALspTree_branch_lenghts
    • improved print_start_time progress reporting from run_ASTRAL and compute_ASTRALspTree_branch_lenghts
  • compiled a static binary of snp-sites. Thanks to Alfredo Hernandez from CCG-UNAM & LCG-UNAM for compiling this binary
  • run_get_phylomarkers_pipeline.sh >= v2.8.1._2024-04-15
    • calls ($bindir/snp-sites-static ) a static binary of snp-sites for Linux (see: bin/linux/snp-sites-static)
    • Updated Dockerfile (v2024-04-18) to avoid installing non-required R packages, generating a significantly lighter image
    • Updated INSTALL.md and README.md
    • updated install_R_deps.R and apt-install_R_dependencies.sh v2024-04-15: replaced devtools for the much lighter remotes; removed uncessary R packages
    • updated .travis.yml v2024-04-15; does not call apt install snp-sites, as it is now provided as static binary in bin/linux/snp-sites-static

Docker image

  1. The GET_PHYLOMARKERS_v2.1.1_2024-04-18 release has the corresponding Docker image v20240418 ready to pull from Docker Hub.
    To pull the latest version of the GET_PHYLOMARKERS Docker image, type: docker pull vinuesa/get_phylomarkers:latest, or docker pull vinuesa/get_phylomarkers:20240418

  2. Docker image v20240418 is significantly lighter (2.0GB), compared to the previous one (v20240414; 2.09GB)

Assets 2