update ghcr container version and add .workflows

.github/workflows/build_container.yml

@@ -0,0 +1,50 @@
+#
+name: Create and publish a Docker image
+
+on:
+  push:
+  workflow_dispatch:
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      # 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: docker
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+

docker/Dockerfile

@@ -46,11 +46,7 @@ RUN add-apt-repository -y ppa:apptainer/ppa \
     && apt install -y apptainer-suid \
     && rm -rf /var/lib/apt/lists/*
 
-
-
-
-
-
+# install applications via conda
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda.sh \
     && bash /miniconda.sh -b -p /opt/miniconda3 \
     && rm -f /miniconda.sh \
@@ -83,5 +79,5 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -
     && echo "conda activate /var/lib/genome-assembly" >> /etc/profile.d/conda.sh
 
 
-    # install jupyterlab 
+# install jupyterlab 
 RUN pip3 --no-cache-dir install jupyterlab

manifest.yml

@@ -1,7 +1,7 @@
 ---
-name: Introduction to Nextflow Workshop
+name: Long-read Genome Assembly
 category: Interactive Apps
 subcategory: Servers
 role: batch_connect
 description: |
-  This app will launch a Jupyter Lab for the Introduction to Nextflow workshop
+  This app will launch a Jupyter Lab for the  Long-read Genome Assembly workshop

submit.yml.erb

@@ -16,8 +16,8 @@ script:
   wall_time: "<%= wall_time.to_i * 3600 %>"
   native:
     container:
-      name: "nextflow"
-      image: "ghcr.io/nesi/training-environment-jupyter-intronextflow-app:v0.2.0"
+      name: "lrgassembly"
+      image: "ghcr.io/nesi/nesi/training-environment-jupyter-lrgassembly-app:v0.1.0"
       command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"]
       working_dir: "<%= Etc.getpwnam(ENV['USER']).dir %>"
       restart_policy: 'OnFailure'

view.html.erb

@@ -1,6 +1,6 @@
 <form action="/node/<%= host %>/<%= port %>/login" method="post" target="_blank">
   <input type="hidden" name="password" value="<%= password %>">
   <button class="btn btn-primary" type="submit">
-    <i class="fa fa-registered"></i> Connect to Intro to Nextflow workshop app
+    <i class="fa fa-registered"></i> Connect to Long-read Genome Assembly workshop app
   </button>
 </form>