diff --git a/images.toml b/images.toml index 650980b..e372de8 100644 --- a/images.toml +++ b/images.toml @@ -24,6 +24,7 @@ peer = '1.3' picard = '2.27.4' reviewer = '0.2.7' reviewer_bw2 = '0.2.7-bw2-fork-0.2' +r-meta = '7.0.0' r-qvalue = '2.34.0' saige-qtl = '8d840248fc025d5f58577ef03a6c23634ee941e5' sambamba = '1.0.1' diff --git a/images/r-meta/Dockerfile b/images/r-meta/Dockerfile new file mode 100644 index 0000000..3b88f78 --- /dev/null +++ b/images/r-meta/Dockerfile @@ -0,0 +1,37 @@ +ARG DRIVER_TAG="1.4" + +FROM australia-southeast1-docker.pkg.dev/analysis-runner/images/driver-base:$DRIVER_TAG + +SHELL ["/bin/bash", "-eo", "pipefail", "-c"] + +ENV MAMBA_ROOT_PREFIX /root/micromamba +ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH + +RUN apt update && \ + # Some R packages require a C compiler during installation. + apt install -y build-essential && \ + rm -r /var/lib/apt/lists/* && \ + rm -r /var/cache/apt/* && \ + wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \ + mkdir $MAMBA_ROOT_PREFIX && \ + micromamba install -y --prefix $MAMBA_ROOT_PREFIX \ + -c cpg -c bioconda -c conda-forge \ + bioconductor-biomart \ + r-argparser \ + r-arrow \ + r-base \ + r-coloc \ + r-devtools \ + r-essentials \ + r-meta \ + r-tidyverse \ + r-viridis && \ + rm -r /root/micromamba/pkgs && \ + pip3 install --no-cache-dir \ + analysis-runner \ + anndata2ri \ + cloudpathlib[all] \ + cpg-utils \ + cpg-workflows \ + gcsfs \ + pandas