From e09fc5858b2a009d7c311bab11a6b4e97639b7b5 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Fri, 8 Dec 2023 13:01:51 -0500 Subject: [PATCH] optimize build layers --- Dockerfile | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1001baf..58127a2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,19 +21,18 @@ RUN apt-get -y -qq install \ 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 \ && 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( 'tidyverse', 'extraDistr', 'LaplacesDemon', 'ade4', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }" +# Install necessary R dependencies for reconstructR that don't have apt packages +RUN R -e "for (lib in c( 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }" +# Rfast in CRAN is broken, install from github RUN R -e "devtools::install_github('RfastOfficial/Rfast', dependencies=TRUE); library(Rfast)" # Install reconstructR R package -- invalidate cache any time github main branch updates