Initial commit

.github/workflows/docker-management.yml

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+# Candace Savonen Oct 2021
+
+name: Docker management
+
+on:
+  pull_request:
+    branches:
+      - 'main'
+    paths: [ docker/Dockerfile ]
+  # This makes it so you can run your github action manually if you choose
+  workflow_dispatch:
+    inputs:
+      dockerhubpush:
+        # We can provide an option to set (we will use this later)
+        description: 'Push to Dockerhub?'
+        required: true
+        default: 'false'
+jobs:
+  docker-management:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      # Set up Docker build
+      - name: Set up Docker Build
+        uses: docker/setup-buildx-action@v1
+
+      # Build the image based on the Dockerfile
+      - name: Build Python Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: false
+          load: true
+          # What directory should this be building from?
+          context: docker
+          # Where's the Dockerfile to build this image from?
+          file: docker/Dockerfile
+          # What should this docker image be called once we are done?
+          tags: jhudsl/reproducible-r
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v1
+        with:
+          # You will need to set up GitHub secrets with your Docker login info
+          # for this to work.
+          # https://docs.github.com/en/actions/security-guides/encrypted-secrets
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+      # This has an if statement so it will only run it we set dockerhubpush to
+      # something not `false` which is the default
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        run: docker push jhudsl/reproducible-r

.github/workflows/run-r-notebook.yml

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+# Candace Savonen Oct 2021
+
+name: Render R Example
+
+# Controls when the action will run. Triggers the workflow on push
+# events only for the master branch
+on:
+  # This makes it so you can run your github action manually if you choose
+  workflow_dispatch:
+  # This is set to run when any pull request is opened to main
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  render-notebooks:
+    # This specifies the docker image it should run on
+    runs-on: ubuntu-latest
+
+    steps:
+      # We need to tell github actions to use the code on the branch we are on
+      - name: checkout
+        uses: actions/checkout@v2
+        with:
+          # How deep should it fetch?
+          fetch-depth: 0
+
+      # Run R analysis
+      - name: Run R analysis example
+      # Here we are telling Docker to run a single command and providing our files
+      # with the --mount argument. We are telling it to run on the jhudsl/reproducible-r
+      # docker image, and then the command we would like to run is `bash run_analysis.sh`
+        run: |
+          docker run \
+          --mount type=bind,target=/home/rstudio,source=$PWD \
+          jhudsl/reproducible-r \
+          bash run_analysis.sh
+
+      - name: Commit rendered R example files
+      # After it runs the analysis, we are having any changed files to be directly
+      # committed to the branch we are working from
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          git add -A
+          git commit -m 'Render R example' || echo "No changes to commit"
+          git push origin || echo "No changes to push"

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.DS_Store
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+.Rprofile
+
+# Ignore renv files
+.local/
+.rstudio/

00-download-data.py

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+# C. Savonen 2021
+
+# https://alexslemonade.github.io/refinebio-py/quickstart.html
+
+import os
+from pathlib import Path
+import pyrefinebio
+
+data_dir = Path('data/SRP070849')
+
+data_file = Path(os.path.join(data_dir, 'SRP070849.tsv'))
+
+metadata_file = Path(os.path.join(data_dir, 'metadata_SRP070849.tsv'))
+
+try:
+  os.mkdir(data_dir, mode = 0o777)
+except OSError as error:
+  print(error)
+
+if not data_file.exists() or not metadata_file.exists():
+
+    print("Downloading SRP070849 from refine.bio")
+
+    pyrefinebio.create_token(agree_to_terms=True, save_token=False)
+
+    pyrefinebio.download_dataset(
+      "data/dataset.zip",
+      "[email protected]",
+      experiments=["SRP070849"],
+      extract=True
+    )