From 0a32319c596a861a524359c9daff87abfdc17add Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Dec 2023 09:35:20 -0500 Subject: [PATCH] switch cran stuff to R install instead of apt --- Dockerfile | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 449f265..89bddce 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,17 +20,20 @@ RUN apt-get -y -qq install \ imagemagick libmagick++-dev \ texlive-base texlive-latex-recommended texlive texlive-latex-extra texlive-extra-utils texlive-fonts-extra \ fonts-roboto \ - r-base r-base-dev r-cran-devtools r-cran-tidyverse r-cran-extradistr \ - r-cran-rcpp r-cran-rcppgsl r-cran-rcppparallel \ - r-cran-segmented r-cran-pixmap r-cran-ape r-cran-seqinr r-cran-ade4 \ + r-base r-base-dev r-cran-devtools \ && apt-get clean +# r-cran-tidyverse r-cran-extradistr \ +# r-cran-rcpp r-cran-rcppgsl r-cran-rcppparallel \ +# r-cran-segmented r-cran-pixmap r-cran-ape r-cran-seqinr r-cran-ade4 \ + + # Set default locale to en_US.UTF-8 RUN locale-gen en_US.UTF-8 ENV LANG="en_US.UTF-8" LANGUAGE="en_US:en" LC_ALL="en_US.UTF-8" # Install necessary R dependencies -RUN R -e "for (lib in c( 'Rfast', 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }" +RUN R -e "for (lib in c( 'tidyverse', 'extradistr', 'Rfast', 'istr', 'LaplacesDemon', 'ade4', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }" # Install reconstructR R package -- invalidate cache any time github main branch updates ADD https://api.github.com/repos/broadinstitute/reconstructR/git/refs/heads/main version.json