Merge pull request #1 from almahmoud/devel

Add shiny build workflow

.github/scripts/galaxy-wrapper-template.xml

@@ -0,0 +1,27 @@
+<tool id="interactivetool_biocshiny_{{{ID}}}" tool_type="interactive" name="{{{NAME}}}" version="0.1">
+    <description>{{{NAME}}} BiocShiny App</description>
+    <requirements>
+        <container type="docker">{{{CONTAINER}}}</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="{{{ID}}}" requires_domain="True">
+            <port>3838</port>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command detect_errors="aggressive">/init</command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        This is an auto-generated wrapper for a BiocShiny application. See source and report issues at {{{SOURCE}}}.
+    </help>
+</tool>

.github/workflows/build_container.yaml

@@ -0,0 +1,62 @@
+name: Build shiny Docker image and generate Galaxy wrapper
+on:
+  workflow_dispatch: {}
+  push: {}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Extract metadata for container image
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value={{branch}}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          platforms: linux/amd64
+
+      - name: Login to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push container image to ghcr
+        uses: docker/build-push-action@v4
+        with:
+          file: Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64
+
+      - name: Set variables
+        id: vars
+        run: |
+          echo "container=${{ steps.meta.outputs.tags }}" >> $GITHUB_OUTPUT
+          echo "source=https://github.com/${{github.repository}}" >> $GITHUB_OUTPUT
+          NAME="$(echo '${{github.repository}}' | awk -F'/' '{print $2}')"
+          echo "name=$NAME" >> $GITHUB_OUTPUT
+          echo "id=$(echo $NAME | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT
+
+      - name: Generate wrapper
+        run: |
+          cp .github/scripts/galaxy-wrapper-template.xml galaxy-wrapper.xml
+          sed -i 's#{{{CONTAINER}}}#${{steps.vars.outputs.container}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{SOURCE}}}#${{steps.vars.outputs.source}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{NAME}}}#${{steps.vars.outputs.name}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{ID}}}#${{steps.vars.outputs.id}}#g' galaxy-wrapper.xml
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add galaxy-wrapper.xml
+          git commit -m "Update Galaxy Wrapper $(TZ=EST date '+%Y-%m-%d_%H-%M')"
+          git push

Dockerfile

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+FROM ghcr.io/bioconductor/shiny:devel as build
+
+RUN chown -R shiny /usr/local/lib/R/site-library && chown -R shiny /usr/local/lib/R/library && rm -rf /srv/shiny-server/sample-apps && curl -o /srv/shiny-server/index.html https://gist.githubusercontent.com/almahmoud/58261d03bfb342274f2e642c4b2ebc4d/raw/4e0271990bce57ae091f622db47b15f8fd89fa29/index.html && mkdir -p /srv/shiny-server/biocshiny && sed -i '/^run_as shiny;/a app_init_timeout 300;\napp_idle_timeout 300;' /etc/shiny-server/shiny-server.conf
+
+COPY --chown=shiny:shiny . /tmp/repo/
+
+USER shiny
+
+RUN cd /tmp/repo && Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)" && Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" && rm -rf /tmp/repo
+
+COPY --chown=shiny:shiny app.R /srv/shiny-server/biocshiny/app.R
+
+USER root
+