PD-2758: Add Slide-tags docker

.github/workflows/build-slide-tags.yml

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+name: SlideTags CI
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
+  pull_request:
+    branches: [ "develop", "master" ]
+    paths:
+      - '3rd-party-tools/slide-tags/**'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      image_tag:
+        description: 'Docker Image Tag (default: branch_name)' 
+
+env:
+  PROJECT_NAME: WARP 3rd Party Tools
+  # Github repo name
+  REPOSITORY_NAME: ${{ github.event.repository.name }}
+  # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
+  DOCKER_REGISTRY: us.gcr.io
+  GCR_PATH: broad-gotc-prod/slide-tags
+  ACR_PATH: slide-tags
+  TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}
+
+  # A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # The job that builds our container
+  build-for-gcr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: 3rd-party-tools/slide-tags
+    # Map a step output to a job output
+    outputs:
+      imagePath: ${{ steps.saveImagePath.outputs.url }}
+    steps:
+    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - uses: actions/checkout@v3
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}
+    - name: Check working directory'
+      run: |
+        echo "Current directory: "
+        pwd
+        ls -lht
+    # Save the image path to an output
+    - id: 'saveImagePath'
+      run: echo "url=${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}" >> $GITHUB_OUTPUT
+    # Log into the Google Docker registry
+    - id: 'Auth'
+      name: Login to GCR
+      uses: docker/login-action@v2
+      with:
+        registry: ${{ env.DOCKER_REGISTRY }}
+        username: _json_key
+        password: ${{ secrets.GCR_CI_KEY }}
+    # Push the image to the Google Docker registry
+    - name: Push image
+      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
+
+  build-for-acr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: 3rd-party-tools/slide-tags
+    steps:
+    # checkout the repo
+    - name: 'Checkout GitHub Action'
+      uses: actions/checkout@v3
+
+    - name: 'Login via Azure CLI'
+      uses: azure/login@v1
+      with:
+        creds: ${{ secrets.AZURE_CREDENTIALS }}
+    - name: 'Build and push image'
+      uses: azure/docker-login@v1
+      with:
+        login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+        username: ${{ secrets.REGISTRY_USERNAME }}
+        password: ${{ secrets.REGISTRY_PASSWORD }}
+    - run: |
+        docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
+        docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}

3rd-party-tools/slide-tags/Dockerfile

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+# 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 Pipeline Development Team <[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 ; \
+
+    # Get spatial count script -- will add this line later when we have a more stable version of the script
+    # wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/main/spatial-count/spatial-count.jl; \
+
+    # 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 /opt https://julialang-s3.julialang.org/bin/linux/x64/1.10/julia-1.10.5-linux-x86_64.tar.gz ; \
+    tar -xzvf /opt/julia-1.10.5-linux-x86_64.tar.gz -C /opt                                        ; \
+    rm /opt/julia-1.10.5-linux-x86_64.tar.gz                                                            ; \
+    ln -s /opt/julia-1.10.5/bin/julia /usr/local/bin/julia ; \
+
+    # Install Julia libraries
+    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 micromamba
+    # curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+    "${SHELL}" <(curl -L micro.mamba.pm/install.sh) 
+
+    # Install python + pip + jupyter
+    # RUN sudo ln -s /usr/bin/python3 /usr/bin/python
+    # RUN sudo apt-get update && sudo apt-get install python3-pip
+    # RUN pip install jupyterlab
+
+# Set tini as default entrypoint
+ENTRYPOINT [ "/sbin/tini", "--" ]