Add custom r-samtools from Dockerfile image

r-samtools/Dockerfile

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+# Use rocker/verse as the base image
+FROM rocker/verse:latest
+
+# Set environment variables for non-interactive installations
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install build tools and dependencies
+RUN apt-get update && apt-get install -y \
+    curl \
+    bzip2 \
+    autoconf \
+    automake \
+    make \
+    gcc \
+    perl \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libssl-dev \
+    libncurses5-dev \
+    libdeflate-dev \
+    libfontconfig1-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libcurl4-openssl-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Download, build, and install samtools
+WORKDIR /usr/local/src
+RUN curl -LO https://github.com/samtools/samtools/releases/download/1.21/samtools-1.21.tar.bz2 \
+    && tar -xjf samtools-1.21.tar.bz2 \
+    && cd samtools-1.21 \
+    && ./configure \
+    && make \
+    && make install \
+    && cd .. && rm -rf samtools-1.21 samtools-1.21.tar.bz2
+
+# Install R packages
+RUN R -e "install.packages(c('devtools', 'remotes', 'BiocManager', 'R.utils'))" \
+    && R -e "BiocManager::install(c('Rsamtools', 'Rbowtie2'))" \
+    && R -e "remotes::install_github(c('ropensci/bold', 'ropensci/taxize'))" \
+    && R -e "devtools::install_github('wejlab/MetaScope')"
+
+# Set working directory
+WORKDIR /home
+
+# Default command
+CMD ["/bin/bash"]

r-samtools/container.yaml

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+docker: jterstriep/r-samtools
+url: https://github.com/ncsa/shpc-registry/
+
+maintainer: 'jterstriep'
+description: R based on rocker/verse image with samtools and matching R packages
+
+latest:
+  '4.4': 'sha256:96b05145a3a68e8c61bd98e7a04682caacf5cb10978d8a7943106ae1e4b920e6'
+tags:
+  '4.4': 'sha256:96b05145a3a68e8c61bd98e7a04682caacf5cb10978d8a7943106ae1e4b920e6'
+
+aliases:
+  ace2sam: /usr/local/bin/ace2sam
+  blast2sam.pl: /usr/local/bin/blast2sam.pl
+  bowtie2sam.pl: /usr/local/bin/bowtie2sam.pl
+  checkbashisms: /usr/local/bin/checkbashisms
+  export2sam.pl: /usr/local/bin/export2sam.pl
+  fasta-sanitize.pl: /usr/local/bin/fasta-sanitize.pl
+  install2.r: /usr/local/bin/install2.r
+  installGithub.r: /usr/local/bin/installGithub.r
+  interpolate_sam.pl: /usr/local/bin/interpolate_sam.pl
+  maq2sam-long: /usr/local/bin/maq2sam-long
+  maq2sam-short: /usr/local/bin/maq2sam-short
+  md5fa: /usr/local/bin/md5fa
+  md5sum-lite: /usr/local/bin/md5sum-lite
+  novo2sam.pl: /usr/local/bin/novo2sam.pl
+  plot-ampliconstats: /usr/local/bin/plot-ampliconstats
+  plot-bamstats: /usr/local/bin/plot-bamstats
+  psl2sam.pl: /usr/local/bin/psl2sam.pl
+  quarto: /usr/local/bin/quarto
+  r: /usr/local/bin/r
+  R: /usr/local/bin/R
+  Rscript: /usr/local/bin/Rscript
+  rserver: /usr/local/bin/rserver
+  rstudio-server: /usr/local/bin/rstudio-server
+  sam2vcf.pl: /usr/local/bin/sam2vcf.pl
+  samtools: /usr/local/bin/samtools
+  samtools.pl: /usr/local/bin/samtools.pl
+  seq_cache_populate.pl: /usr/local/bin/seq_cache_populate.pl
+  soap2sam.pl: /usr/local/bin/soap2sam.pl
+  wgsim: /usr/local/bin/wgsim
+  wgsim_eval.pl: /usr/local/bin/wgsim_eval.pl
+  zoom2sam.pl: /usr/local/bin/zoom2sam.pl