Release GET_PHYLOMARKERS_v2.2.1_2024-04-18 · vinuesa/get_phylomarkers

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

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