From f5f0675ff5acd9925ed814d465209837eaa06279 Mon Sep 17 00:00:00 2001 From: vinuesa Date: Sat, 13 Apr 2024 19:28:42 -0600 Subject: [PATCH] Dockerfile v2024-04-13 now installs snp-sites in the 'apt install' call --- Dockerfile | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 76f311b..246ca5a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,12 +1,16 @@ -## Dockerfile version 2024-04-01, based on v2022-11-19 +## Dockerfile version 2024-04-13, based on v2022-11-19 # - build images using as context the cloned get_phylomarkers GitHub repository # based on latest ubuntu (jammy) and r-base (4.2.2) # - runs 22 tests during the final image's build stage & sets ENV R_LIBS_SITE + +# Check versions: https://hub.docker.com/_/ubuntu FROM ubuntu:latest + +#Check versions and compatibility with ubuntu releases at https://github.com/rstudio/r-docker FROM rstudio/r-base:4.2.2-jammy LABEL authors="Pablo Vinuesa and Bruno Contreras Moreira " -LABEL keywods="bioinformatics, genomics, phylogenetics, phylogenomics, species tree, core-genome, pan-genome, maximum likelihood, parsimony, population genetics, molecular clock, Docker image" +LABEL keywods="bioinformatics, genomics, phylogenetics, phylogenomics, species tree, core-genome, pan-genome, maximum likelihood, parsimony, population genetics, molecular clock, Docker image, pipeline" LABEL version="20240401" LABEL description="Ubuntu 22.04 + Rstudio/r-base 4.2.2 based image of GET_PHYLOMARKERS" LABEL summary="This image runs GET_PHYLOMARKERS for advanced and versatile phylogenomic analysis of microbial pan-genomes" @@ -31,6 +35,7 @@ libssl-dev \ make \ parallel \ wget \ +snp-sites \ && apt clean && apt purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && cpanm Term::ReadLine ## mkdir get_phylomarkes in /, copy all contents into it; make it the working directory & install required R packages @@ -123,7 +128,7 @@ CMD ["/bin/bash"] # $ cd ~/data/pan_genome # $ estimate_pangenome_phylogenies.sh -f pangenome_matrix_t0.fasta -r 1 -S UFBoot -## Thorough functional testing (8 tests calling the two main scripts) can also be run automatically as follows, +## Thorough functional testing (9 tests calling the two main scripts) can also be run automatically as follows, # assuming that you have copied the core_genome and pan_genome test sequences to the data directory, as indicated above. # $ cd && run_test_suite.sh /home/you/data