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docker build fixes #2

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merged 7 commits into from
Dec 8, 2023
Merged

docker build fixes #2

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0a32319
switch cran stuff to R install instead of apt
dpark01 Dec 8, 2023
ee40773
typo capitalization
dpark01 Dec 8, 2023
6370e1a
Rfast install bug https://github.com/RfastOfficial/Rfast/issues/3
dpark01 Dec 8, 2023
0466392
non-existent package?
dpark01 Dec 8, 2023
e09fc58
optimize build layers
dpark01 Dec 8, 2023
ce8b76c
dont upgrade dependencies
dpark01 Dec 8, 2023
c6ca701
revert: underlying libraries need upgrade
dpark01 Dec 8, 2023
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9 changes: 6 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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