r-meta dockerfile for meta-analysis (#141)

* r-meta dockerfile for meta-analysis

* EOF

* remove qvalue

* add coloc

---------

Co-authored-by: Matt Welland <mattwellie@gmail.com>

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'

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