push more R dependencies earlier in the Dockerfile to improve build s…

…peed and layer caching

Dockerfile

@@ -16,17 +16,22 @@ RUN apt-get update && \
 RUN apt-get -y -qq install \
     less nano vim git wget curl jq zstd parallel locales \
     gnupg libssl-dev libcurl4-openssl-dev \
-    libxml2 libxml2-dev \
+    libgsl-dev libxml2 libxml2-dev \
     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-rcpp r-cran-ape \
+    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
 
 # 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 "install.packages(c( 'Rfast', 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect' ), dependencies=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
 RUN R -e "devtools::install_github('broadinstitute/reconstructR', dependencies=TRUE, upgrade='never')"