Changed github URLs and added Dockerfile and GitHub actions

.github/workflows/docker-publish.yml

@@ -0,0 +1,89 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  schedule:
+    - cron: '32 5 * * *'
+  push:
+    branches: [ "main" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Install the cosign tool except on PR
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        with:
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # Login against a Docker registry except on PR
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Lowercase repo variable
+      - name: Downcase REPO variable
+        run: |
+          echo "IMAGE_NAME=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
+
+      # Extract metadata (tags, labels) for Docker
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

Dockerfile

@@ -0,0 +1,53 @@
+FROM rocker/r-ver:4.5.2
+
+# System dependencies
+RUN apt-get update -y && apt-get install -y \
+    make \
+    pkg-config \
+    libpcre2-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libicu-dev \
+    libcurl4-openssl-dev \
+    libfftw3-dev \
+    pandoc \
+    zlib1g-dev \
+    libjpeg-dev \
+    libpng-dev \
+    default-jdk \
+    libtiff-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# rJava configuration
+RUN R CMD javareconf
+
+# R and renv setup
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+
+# Change to workdir
+WORKDIR /srv/shiny-server/
+
+# Copy renv
+COPY Shiny/renv /srv/shiny-server/renv
+COPY Shiny/.Rprofile /srv/shiny-server/.Rprofile
+COPY Shiny/renv.lock /srv/shiny-server/renv.lock
+
+# Env configuration
+ENV RENV_PATHS_CACHE=/root/.cache/R/renv
+ENV RENV_CONFIG_CACHE_SYMLINKS=false
+ENV HOME=/home/
+
+# Run renv::restore()
+RUN  R -e 'source("renv/activate.R")'
+RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()'
+
+# Copy Shiny app
+COPY Shiny/ij /srv/shiny-server/ij
+COPY Shiny/www /srv/shiny-server/www
+COPY Shiny/app.R /srv/shiny-server/app.R
+COPY Shiny/Functions.R /srv/shiny-server/Functions.R
+COPY Example_images/ /srv/Example_images/
+
+# Expose and run
+EXPOSE 3838
+CMD ["R", "-e", "shiny::runApp('/srv/shiny-server', host='0.0.0.0', port=3838)"]

Shiny/app.R

@@ -37,7 +37,7 @@ ui <- fluidPage(
             align = "rigth",
             height = 80
           ),
-          href = "https://github.com/antotartier/FAB-gal",
+          href = "https://github.com/GenCanAgeLab/FAB-gal",
           target = "_blank"
         )
       ),
@@ -222,7 +222,7 @@ ui <- fluidPage(
         actionButton('run.all', "Run for all images", class = "btn-primary"),
         a(
           "Click Here To Learn More",
-          href = "https://github.com/antotartier/FAB-gal/wiki",
+          href = "https://github.com/GenCanAgeLab/FAB-gal/wiki",
           target = "_blank",
           class = "btn btn-info",
           icon = icon("info-circle")
@@ -312,7 +312,7 @@ ui <- fluidPage(
     ),
     a(
       "github.com/GenCanAgeLab/SAbGal_quant",
-      href = "https://github.com/antotartier/FAB-gal",
+      href = "https://github.com/GenCanAgeLab/FAB-gal",
       target = "_blank"
     )
   ),