Merge pull request #105 from olliecheng/docker_images

Updated Dockerfile for easier deployment and consistent builds

.dockerignore

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+.gitignore
+.git/
+Dockerfile
+**/*.md

.github/workflows/create_docker_image.yml

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+# This Action is adapted from the GitHub Docs, located at:
+# http://docs.github.com/en/actions/publishing-packages/publishing-docker-images#publishing-images-to-github-packages
+
+name: "Publish JAFFA Docker image"
+
+# Configures this workflow to run every time a change is pushed to the branch called `release`.
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'JAFFA version to tag with'
+        required: true
+      latest:
+        description: 'Set the :latest Docker tag. Only enable for release builds, as it is recommended that users install the software at the :latest tag.'
+        required: true
+        default: true
+        type: boolean
+
+# 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 }}
+
+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
+      attestations: write
+      id-token: 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: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # 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@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value=latest,priority=1000,enable=${{ github.event.inputs.latest }}
+            type=raw,value=${{ github.event.inputs.version }},priority=900
+            type=sha,prefix={{branch}}-
+
+      # 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
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

Dockerfile

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+# syntax=docker/dockerfile:1
+
+# must use bookworm for directly compatible R version >=4.4.0
+FROM debian:bullseye-slim AS base
+
+# get latest version of R: https://cran.r-project.org/bin/linux/debian/
+RUN apt-get update
+RUN apt-get install -y gnupg2
+RUN apt-get install -y perl python3
+
+# set locale
+RUN apt-get install -y locales
+RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
+ENV LANG=en_US.UTF-8
+ENV LC_ALL=en_US.UTF-8
+
+RUN gpg --keyserver keyserver.ubuntu.com \
+    --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'
+RUN gpg --armor --export '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' | \
+    tee /etc/apt/trusted.gpg.d/cran_debian_key.asc
+
+RUN echo 'deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/' >> /etc/apt/sources.list
+
+RUN apt-get update
+
+# fix version of Java for bpipe 0.9.9.2
+RUN apt-get install -y r-base-core r-bioc-iranges openjdk-11-jre --no-install-recommends
+
+# install libncurses.so.6 for minimap2
+RUN apt-get install -y libncurses6 --no-install-recommends
+
+
+FROM base AS build
+# install useful tools for building non-R software
+# this is placed after the R installs so that they can
+# be cached
+RUN apt-get install -y build-essential wget make cmake unzip zip python3 zlib1g-dev libncurses-dev
+
+
+WORKDIR /JAFFA
+
+COPY ./install_linux64.sh .
+COPY ./src ./src
+
+RUN ./install_linux64.sh
+
+COPY . .
+
+# set a reference file path to /ref for easy binding
+RUN sed -i 's/refBase = codeBase/refBase = "\/ref"/' JAFFA_stages.groovy
+
+# we only need this to run the image
+FROM base
+
+LABEL org.opencontainers.image.title "JAFFA" \
+      org.opencontainers.image.description "High sensitivity transcriptome-focused fusion gene detection." \
+      org.opencontainers.image.authors "Davidson, N.M., Majewski, I.J. & Oshlack, A." \
+      org.opencontainers.image.source "https://github.com/Oshlack/JAFFA" \
+      org.opencontainers.image.documentation "https://github.com/Oshlack/JAFFA/wiki/HowToSetUpJAFFA#docker"
+
+
+COPY --from=build /JAFFA /JAFFA
+# RUN strip --strip-debug /usr/local/lib/R/site-library/*/libs/*.so
+
+RUN apt remove -y gcc
+RUN apt autoremove
+
+ENV PATH=${PATH}:/JAFFA/tools/bin:/JAFFA
+
+ENTRYPOINT ["/JAFFA/tools/bin/bpipe", "run"]