Add slidetag

broadinstitute · Oct 4, 2024 · c8b6661 · c8b6661
1 parent dfa6b3b
commit c8b6661
Showing 1 changed file with 91 additions and 0 deletions.
diff --git a/3rd-party-tools/slidetag-spatial/Dockerfile b/3rd-party-tools/slidetag-spatial/Dockerfile
@@ -0,0 +1,91 @@
+# Taken from https://github.com/MacoskoLab/Macosko-Pipelines/blob/main/positioning/Dockerfile
+# Modified slightly to reduce the number of layers
+
+FROM debian:bookworm
+SHELL ["/bin/bash", "-c"]
+
+LABEL MAINTAINER="Broad Institute DSDE <[email protected]"
+
+# Install system libraries
+RUN apt-get update ; \
+    apt-get install -y --no-install-recommends zip unzip gzip less wget curl    ; \
+    apt-get install -y --no-install-recommends sudo tmux htop dstat socat       ; \
+    apt-get install -y --no-install-recommends procps moreutils gnupg           ; \
+    apt-get install -y --no-install-recommends gdebi-core build-essential alien ; \
+    apt-get install -y --no-install-recommends libhdf5-dev hdf5-tools libpng-dev libtiff5-dev libjpeg-dev ; \
+    apt-get install -y --no-install-recommends apt-transport-https ca-certificates libssl-dev libxml2-dev zlib1g-dev ; \
+    apt-get install -y --no-install-recommends libfreetype6-dev libcairo2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev ; \
+
+    # Install Google Cloud SDK
+    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo gpg --dearmor -o /usr/share/keyrings/cloud.google.gpg && apt-get update -y && apt-get install google-cloud-sdk -y ;\
+
+    # Install Rust
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y ; \
+    # Install Julia
+    wget -P /software https://julialang-s3.julialang.org/bin/linux/x64/1.10/julia-1.10.5-linux-x86_64.tar.gz ; \
+    tar -xzvf /software/julia-1.10.5-linux-x86_64.tar.gz -C /software                                        ; \
+    rm /software/julia-1.10.5-linux-x86_64.tar.gz                                                            ; \
+    ln -s /software/julia-1.10.5/bin/julia /usr/local/bin/julia ; \
+
+    # Install Julia libraries
+    RUN julia -e 'using Pkg;                     \
+                  Pkg.add(["CSV",                \
+                       "GZip",               \
+                       "SIMD",               \
+                       "HDF5",               \
+                       "Plots",              \
+                       "FASTX",              \
+                       "Peaks",              \
+                       "IJulia",             \
+                       "ArgParse",           \
+                       "CodecZlib",          \
+                       "PDFmerger",          \
+                       "IterTools",          \
+                       "StatsBase",          \
+                       "DataFrames",         \
+                       "StatsPlots",         \
+                       "StringViews",        \
+                       "Combinatorics",      \
+                       "Distributions",      \
+                       "LinearAlgebra",      \
+                       "LoopVectorization"])' ; \
+
+    # Install R
+    export R_VERSION=4.3.3 ; \
+    curl -O https://cdn.rstudio.com/r/debian-12/pkgs/r-${R_VERSION}_1_amd64.deb ; \
+    echo y | gdebi r-${R_VERSION}_1_amd64.deb                                   ; \
+    sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R                       ; \
+    sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript 	   ; \
+
+    # Install R libraries
+    R -e "install.packages(c('qs',          \
+                             'glue',        \
+                             'qpdf',        \
+                             'dplyr',       \
+                             'purrr',       \
+                             'furrr',       \
+                             'rlist',       \
+                             'rdist',       \
+                             'tidyr',       \
+                             'hdf5r',       \
+                             'dbscan',      \
+                             'future',      \
+                             'Seurat',      \
+                             'cowplot',     \
+                             'ggplot2',     \
+                             'ggrastr',     \
+                             'stringr',     \
+                             'viridis',     \
+                             'jsonlite',    \
+                             'magrittr',    \
+                             'gridExtra',   \
+                             'SeuratObject'), repos='http://cran.rstudio.com/')" ; \
+
+    R -e "if (!require('BiocManager',quietly=T)) {install.packages('BiocManager',repos='http://cran.rstudio.com/')}; \
+          BiocManager::install('rhdf5')"
+
+    # Install python
+    # TODO
+
+# Set tini as default entrypoint 
+ENTRYPOINT [ "/sbin/tini", "--" ]