Merge pull request #4 from satijalab/add_seurat-ci

Add Dockerfile for `satijalab/seurat-ci` Image

Author: dcollins15

seurat-ci/Dockerfile

@@ -0,0 +1,72 @@
+# Dockerfile for the `satijalab/seurat-ci` image, intended for running CI 
+# workflows for https://github.com/satijalab/seurat and its related projects 
+# (e.g. https://github.com/satijalab/seurat-object).
+
+# Use `rocker/r2u` as the base image.
+# The r2u Project provides precompiled Ubuntu binaries for all CRAN packages 
+# and their BioConductor dependencies accessible via `apt`. With `bspm` enabled, 
+# calls to `install.packages` can also take advantage of this configuration. 
+# The main advantage of this setup is that installs are faster and more 
+# reliable. The downside is that since r2u only makes precompiled binaries 
+# available for R-release, this setup is not compatible with any other versions 
+# of R. See https://eddelbuettel.github.io/r2u/ for more details.
+FROM rocker/r2u:jammy
+
+# Set a CTAN mirror and add `texlive` to the PATH.
+ENV CTAN_REPO="https://mirror.ctan.org/systems/texlive/tlnet"
+ENV PATH="$PATH:/usr/local/texlive/bin/linux"
+
+# In addition to `rocker/r2u` images, the Rocker Project also provides a 
+# set of images that comes with a set of shared setup scripts providing tools 
+# from `pandoc` and `texlive` to `python` and `CUDA`, for more details, see
+# https://github.com/rocker-org/rocker-versioned2?tab=readme-ov-file#rocker-scripts.
+#
+# Using multi-stage builds we can pull these scripts direclty from the 
+# `rocker/r-ver` image and use them to install the things we need.
+#
+# TODO: consider vendorizing rocker_scripts/ directy into seurat-docker 
+# and introducing a workflow to keeps its contents in sync with 
+# https://github.com/rocker-org/rocker-versioned2/tree/master/scripts.
+COPY --from=rocker/r-ver:latest /rocker_scripts/bin/ /rocker_scripts/bin/
+COPY --from=rocker/r-ver:latest /rocker_scripts/install_pandoc.sh /rocker_scripts/install_pandoc.sh
+COPY --from=rocker/r-ver:latest /rocker_scripts/install_texlive.sh /rocker_scripts/install_texlive.sh
+RUN apt update \
+    && apt install -y --no-install-recommends \ 
+        # System dependencies not covered by the copied scripts.
+        texinfo \
+        tidy \
+        # R packages (brought to you by r2u).
+        r-cran-devtools \
+        r-cran-plotly \
+        r-cran-v8 \
+    # The `install2.r` script comes from the `littler` package and is included 
+    # under `/usr/local/bin/` by the base image. The version found under 
+    # `/rocker_scripts/bin/install2.r` differs from the `littler` version in 
+    # two ways:
+    #   1. It does not provide a `--type` flag
+    #   2. It exposes an additional `--skipmissing` flag
+    # Neither flag is actually used in the following scripts but it's probably 
+    # best to make sure that we're using the intended version just to be safe.
+    && ln -sf /rocker_scripts/bin/install2.r /usr/local/bin/install2.r \
+    && /rocker_scripts/install_pandoc.sh \
+    && /rocker_scripts/install_texlive.sh
+
+# Install `BPCells`. Since it is not available on CRAN or BioConductor, the 
+# package needs to be installed from source. This is quite slow, hence why
+# this is the only `Seurat` dependency being explicitly pre-installed. 
+RUN apt update \
+    && apt install -y libhdf5-dev \ 
+    && Rscript -e 'install.packages("BPCells", repos = "https://bnprks.r-universe.dev")'
+
+# Set environment variables to suppress NOTEs that are accepted by CRAN, see
+# https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck
+# for more details. 
+ENV _R_CHECK_PKG_SIZES_="false"
+ENV _R_CHECK_RD_XREFS_="false"
+ENV _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_="false"
+ENV _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_="true"
+
+# Remove scripts copied from `rocker/r-ver` and point /usr/local/bin/install2.r 
+# back to the littler version. 
+RUN ln -sf /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
+    && rm -rf /rocker_scripts/