Add Dockerfile for rocker-seurat 4.4.1-5.1.0

Unpinned some versions
MonashBioinformaticsPlatform · Aug 17, 2024 · e257ec0 · e257ec0
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commit e257ec0
Showing 1 changed file with 79 additions and 0 deletions.
diff --git a/dockerfiles/rocker-seurat/4.4.1-5.1.0/Dockerfile b/dockerfiles/rocker-seurat/4.4.1-5.1.0/Dockerfile
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+FROM ghcr.io/rocker-org/rstudio:4.4.1
+
+# This exists as an image at: https://ghcr.io/monashbioinformaticsplatform/rocker-ultra/rocker-seurat:latest
+#
+# Build like:
+#
+#   docker buildx build --platform linux/amd64 \
+#     -t ghcr.io/monashbioinformaticsplatform/rocker-ultra/rocker-seurat:latest \
+#     -t ghcr.io/monashbioinformaticsplatform/rocker-ultra/rocker-seurat:4.4.1-5.1.0 \
+#     -f Dockerfile .
+#
+# where 4.4.1 is the R version, 5.1.0 is the Seurat version
+
+# See layers used at: https://hub.docker.com/r/satijalab/seurat
+#                     https://github.com/satijalab/seurat-docker/blob/master/latest/Dockerfile
+
+ARG SEURAT_VERS=5.1.0
+ARG QUARTO_VERS=1.5.56
+
+# https://rocker-project.org/images/versioned/r-ver#switch-the-default-cran-mirror
+#ARG CRAN="https://cloud.r-project.org"
+ARG CRAN="https://mirror.aarnet.edu.au/pub/CRAN/"
+ARG BIOC_MIRROR="https://bioconductor.org"
+
+RUN echo "options(repos = c(CRAN = '${CRAN}'))" >>"${R_HOME}/etc/Rprofile.site"
+RUN echo "options(BioC_mirror = '${BIOC_MIRROR}')" >>"${R_HOME}/etc/Rprofile.site"
+
+RUN apt-get update && \
+    apt-get install --yes \
+            build-essential git pkg-config wget curl htop pandoc \
+            libhdf5-dev libcurl4-openssl-dev libssl-dev libpng-dev libboost-all-dev \
+            libxml2 libxml2-dev openjdk-8-jdk python3-dev python3-pip libfftw3-dev libgsl-dev \
+            llvm \
+            libglpk40 libglpk-dev libigraph-dev libigraph2 libfontconfig1-dev libcairo2-dev \
+            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libsqlite0-dev \
+            gfortran \
+            libbz2-dev libsuperlu-dev libarpack2-dev libxt-dev tcl8.6-dev tk8.6-dev \
+            texinfo texlive-fonts-extra libtiff5-dev libpango1.0-dev freeglut3-dev libxmu-dev \
+            libglu1-mesa-dev libcgal-dev libnetcdf-dev libudunits2-0 libmagick++-dev \
+            libboost-iostreams-dev libboost-log-dev libboost-system-dev libboost-test-dev \
+            libpcre2-dev libgit2-dev libharfbuzz-dev libfribidi-dev libjpeg62 liborc-0.4-0 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install UMAP
+RUN LLVM_CONFIG=/usr/lib/llvm-14/bin/llvm-config pip3 install llvmlite && \
+    pip3 install numpy && \
+    pip3 install umap-learn
+
+RUN git clone --branch v1.2.1 https://github.com/KlugerLab/FIt-SNE.git && \
+    cd FIt-SNE && g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp  -o /usr/bin/fast_tsne -pthread -lfftw3 -lm -Wno-address-of-packed-member
+
+RUN wget "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERS}/quarto-${QUARTO_VERS}-linux-amd64.deb" && \
+    apt install -y ./quarto-${QUARTO_VERS}-linux-amd64.deb && \
+    rm quarto-${QUARTO_VERS}-linux-amd64.deb
+
+RUN R --no-echo --no-restore --no-save -e "install.packages(c('devtools', 'remotes', 'renv', 'R.utils'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('BiocManager'))" && \
+    R --no-echo --no-restore --no-save -e "BiocManager::install(version = '3.19')" && \
+    R --no-echo --no-restore --no-save -e "BiocManager::install(c(\
+        'multtest', 'S4Vectors', 'SummarizedExperiment', 'SingleCellExperiment', \
+        'MAST', 'DESeq2', 'BiocGenerics', 'GenomicRanges', 'IRanges', 'rtracklayer', 'monocle', 'Biobase', 'limma', \
+        'glmGamPoi', 'DelayedArray', 'DelayedMatrixStats', 'lme4', 'batchelor', 'HDF5Array', 'terra', 'ggrastr' \
+    ))" && \
+    R --no-echo --no-restore --no-save -e "BiocManager::install(c('celldex', 'SingleR'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('Matrix.utils'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('VGAM', 'R.utils', 'metap', 'Rfast2', 'ape', 'enrichR', 'mixtools'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('spatstat.explore', 'spatstat.geom'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('hdf5r'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('evaluate', 'highr', 'knitr', 'markdown', 'rmarkdown', 'tinytex', 'xfun'))" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('rgeos'))" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_version('Seurat', version = '${SEURAT_VERS}')" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_github('mojaveazure/seurat-disk')" && \
+    R --no-echo --no-restore --no-save -e "devtools::install_github('cole-trapnell-lab/monocle3')" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_version('RcppArmadillo')" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_version('harmony', upgrade='never')" && \
+    R --no-echo --no-restore --no-save -e "install.packages(c('clustree', 'RColorBrewer'))" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_github('plotly/plotly.R')" && \
+    R --no-echo --no-restore --no-save -e "remotes::install_github('pfh/langevitour')"