added biomart for excon

.github/workflows/push-biomart.yml

@@ -0,0 +1,43 @@
+name: Build biomart
+
+on:
+  workflow_dispatch
+
+#When updating images change image tag below to correspond to changes
+env:
+  IMAGE_NAME: biomart_perl
+  IMAGE_TAG: r-4.3.3_perl-5.38.2 
+
+jobs:
+  build:
+    name: Build
+    #Using ubuntu-22.04 instead of ubuntu-latest to use Docker 24 instead of Docker 25 as it causes gitpod issues
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Clean workspace before start
+      run: rm -rf $GITHUB_WORKSPACE/*
+
+    - uses: actions/[email protected]
+
+    - name: Check Docker version
+      run: docker --version
+
+    - name: Build image
+      id: build-image
+      run: docker build -t ${IMAGE_NAME}:${IMAGE_TAG} -f ${IMAGE_NAME}/Dockerfile . 
+
+    - name: Quay.io login
+      run: docker login -u ${{ secrets.DOCKERBUILD_ROBOT_USERNAME }} --password-stdin <<< ${{ secrets.DOCKERBUILD_ROBOT_PASSWORD }} quay.io
+
+    - name: Tag image
+      run: docker tag ${IMAGE_NAME}:${IMAGE_TAG} quay.io/ecoflowucl/${IMAGE_NAME}:${IMAGE_TAG}
+
+    - name: Push image
+      run: docker push quay.io/ecoflowucl/${IMAGE_NAME}:${IMAGE_TAG}
+
+    - name: Remove docker config
+      run: rm -rf /home/runner/.docker
+
+    - name: Clean workspace after finish
+      run: rm -rf $GITHUB_WORKSPACE/*

biomart_perl/Dockerfile

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+FROM rocker/r-base:4.3.3
+
+RUN apt-get update && \
+    apt-get install -y procps perl && \
+    apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+RUN Rscript -e "install.packages('BiocManager')"
+
+RUN Rscript -e "BiocManager::install('biomaRt')"
+
+CMD ["/bin/bash"]