diff --git a/Dockerfile b/Dockerfile index 449f265..58127a2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,7 +20,8 @@ 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-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 @@ -29,8 +30,10 @@ RUN apt-get -y -qq install \ 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) }" +# 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 ADD https://api.github.com/repos/broadinstitute/reconstructR/git/refs/heads/main version.json