bixbeta/dnabarcodes repository overview

FROM rocker/r-ver:4.4.2

⁠System dependencies

RUN apt-get update && apt-get install -y --no-install-recommends
wget
libcurl4-openssl-dev
libssl-dev
libxml2-dev
libfontconfig1-dev
libfreetype6-dev
libharfbuzz-dev
libfribidi-dev
libpng-dev
libtiff5-dev
libjpeg-dev
imagemagick
ghostscript
openssh-client
pandoc
&& rm -rf /var/lib/apt/lists/*
&& sed -i 's/rights="none" pattern="PDF"/rights="read|write" pattern="PDF"/' /etc/ImageMagick-6/policy.xml

⁠Quarto (pinned for reproducibility; detects arm64 vs amd64 automatically)

ARG QUARTO_VERSION=1.5.57 RUN ARCH=$(dpkg --print-architecture)
&& wget -q https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${ARCH}.deb⁠
&& dpkg -i quarto-${QUARTO_VERSION}-linux-${ARCH}.deb
&& rm quarto-${QUARTO_VERSION}-linux-${ARCH}.deb

⁠Point rmarkdown at Quarto's bundled pandoc (avoids "pandoc not found" errors)

ENV RSTUDIO_PANDOC=/opt/quarto/bin/tools

⁠Use Posit Package Manager for pre-built Linux binaries (Ubuntu 24.04 noble)

⁠This avoids source compilation failures (cmake, boost, etc.)

ENV RSPM="https://packagemanager.posit.co/cran/__linux__/noble/latest⁠"

⁠CRAN packages

RUN R -e "install.packages(c('BiocManager','dplyr','progress','tibble','tidyr',
'ggplot2','ggrepel','matrixStats','DT','viridisLite','reshape2',
'RColorBrewer','knitr','rmarkdown','amap','xtable',
'kableExtra','GGally','ggdendro','gridExtra'),
repos=Sys.getenv('RSPM'), Ncpus=4)"

⁠Bioconductor dependencies required by SARTools 1.7.4

RUN R -e "options(repos = Sys.getenv('RSPM'));
BiocManager::install(c('DESeq2','edgeR','biomaRt',
'genefilter','limma', 'DNABarcodes'), ask=FALSE, Ncpus=4)"

⁠Install pinned SARTools 1.7.4 from local tarball

COPY SARTools-1.7.4.tar.gz /tmp/ RUN R CMD INSTALL /tmp/SARTools-1.7.4.tar.gz
&& rm /tmp/SARTools-1.7.4.tar.gz