Development

.github/workflows/dockerhub-on-version.yml

@@ -0,0 +1,139 @@
+name: Build & Push Docker image on package version change
+
+on:
+  push:
+    branches: [ main, vcf_sanity_check ]
+    paths:
+      - .github/workflows/dockerhub-on-version.yml
+      - Dockerfile
+      - DESCRIPTION
+  workflow_dispatch:
+
+concurrency:
+  group: docker-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  IMAGE: docker.io/breedinginsight/bigapp
+  IMAGE_DEPS: docker.io/breedinginsight/bigapp-deps
+  DEPS_TAG: r4.5-bioc3.21-2025-08
+
+jobs:
+  check-version:
+    runs-on: ubuntu-latest
+    outputs:
+      changed: ${{ steps.ver.outputs.changed }}
+      version: ${{ steps.ver.outputs.version }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - id: ver
+        shell: bash
+        run: |
+          set -euo pipefail
+          cur_ver=$(sed -n 's/^Version:[[:space:]]*//p' DESCRIPTION | tr -d '[:space:]')
+          prev_sha="${{ github.event.before }}"
+          if git show "${prev_sha}:DESCRIPTION" >/dev/null 2>&1; then
+            prev_ver=$(git show "${prev_sha}:DESCRIPTION" | sed -n 's/^Version:[[:space:]]*//p' | tr -d '[:space:]')
+          else
+            prev_ver=""
+          fi
+          changed=false
+          if [[ -z "${prev_ver}" || "${cur_ver}" != "${prev_ver}" ]]; then changed=true; fi
+          echo "version=${cur_ver}" >> "$GITHUB_OUTPUT"
+          echo "changed=${changed}" >> "$GITHUB_OUTPUT"
+
+  build-amd64:
+    needs: check-version
+    if: needs['check-version'].outputs.changed == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-qemu-action@v3
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE }}
+          tags: |
+            type=raw,value=v${{ needs['check-version'].outputs.version }}-amd64
+            type=raw,value=sha-${{ github.sha }}-amd64
+      - name: Build & push app (amd64)
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile
+          platforms: linux/amd64
+          push: true
+          build-args: |
+            BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: |
+            type=registry,ref=${{ env.IMAGE }}:buildcache-amd64
+          cache-to: type=registry,ref=${{ env.IMAGE }}:buildcache-amd64,mode=max,compression=zstd
+
+  build-arm64:
+    needs: check-version
+    if: needs['check-version'].outputs.changed == 'true' 
+    continue-on-error: true
+    runs-on: ubuntu-latest
+    timeout-minutes: 350
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-qemu-action@v3
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE }}
+          tags: |
+            type=raw,value=v${{ needs['check-version'].outputs.version }}-arm64
+            type=raw,value=sha-${{ github.sha }}-arm64
+      - name: Build & push app (arm64)
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile
+          platforms: linux/arm64
+          push: true
+          build-args: |
+            BASE_IMAGE=${{ env.IMAGE_DEPS }}:${{ env.DEPS_TAG }}
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: |
+            type=registry,ref=${{ env.IMAGE }}:buildcache-arm64
+          cache-to: type=registry,ref=${{ env.IMAGE }}:buildcache-arm64,mode=max,compression=zstd
+
+  manifest:
+    needs: [check-version, build-amd64, build-arm64]
+    if: >
+      needs['check-version'].outputs.changed == 'true' &&
+      needs['build-amd64'].result == 'success' &&
+      needs['build-arm64'].result == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Create multi-arch manifest
+        env:
+          IMAGE: ${{ env.IMAGE }}
+          PKG_VERSION: ${{ needs['check-version'].outputs.version }}
+        run: |
+          set -euo pipefail
+          docker buildx imagetools create \
+            -t "$IMAGE:v${PKG_VERSION}" \
+            -t "$IMAGE:latest" \
+            "$IMAGE:v${PKG_VERSION}-amd64" \
+            "$IMAGE:v${PKG_VERSION}-arm64"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BIGapp
 Title: Breeding Insight Genomics Shiny Application
-Version: 1.3.0
+Version: 1.5.1
 Authors@R: 
     c(
               person(c("Alexander", "M."), "Sandercock",
@@ -73,6 +73,6 @@ Imports:
     methods
 Remotes:
     github::jendelman/GWASpoly,
-    github::Breeding-Insight/BIGr,
+    bioc::Rsamtools
 Suggests:
     testthat

Dockerfile

@@ -1,47 +1,25 @@
-FROM rocker/r-ver:4.4.2
-RUN apt-get update && apt-get install -y  cmake libz-dev libcurl4-openssl-dev libssl-dev
-RUN R -e 'install.packages("remotes")'
-RUN Rscript -e 'remotes::install_version("adegenet",upgrade="never", version = "2.1.10")'
-RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
-RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.33")'
-RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.4")'
-RUN Rscript -e 'remotes::install_version("vcfR",upgrade="never", version = "1.15.0")'
-RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.5.1")'
-RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.3.1")'
-RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
-RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.9.1")'
-RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
-RUN Rscript -e 'remotes::install_version("bs4Dash",upgrade="never", version = "2.3.4")'
-RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.5.1")'
-RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "1.0.2")'
-RUN Rscript -e 'remotes::install_version("markdown",upgrade="never", version = "1.13")'
-RUN Rscript -e 'remotes::install_version("scales",upgrade="never", version = "1.3.0")'
-RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.4")'
-RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.8.7")'
-RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
-RUN Rscript -e 'remotes::install_version("shinydisconnect",upgrade="never", version = "0.1.1")'
-RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "3.1.0")'
-RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.1")'
-RUN Rscript -e 'remotes::install_version("updog",upgrade="never", version = "2.1.5")'
-RUN Rscript -e 'remotes::install_version("AGHmatrix",upgrade="never", version = "2.1.4")'
-RUN Rscript -e 'remotes::install_version("factoextra",upgrade="never", version = "1.0.7")'
-RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.7")'
-RUN Rscript -e 'remotes::install_version("future",upgrade="never", version = "1.34.0")'
-RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.1.0")'
-RUN Rscript -e 'remotes::install_version("RColorBrewer",upgrade="never", version = "1.1.3")'
-RUN Rscript -e 'remotes::install_version("tibble",upgrade="never", version = "3.2.1")'
-RUN Rscript -e 'remotes::install_version("rrBLUP",upgrade="never", version = "4.6.3")'
-RUN Rscript -e 'remotes::install_version("MASS",upgrade="never", version = "7.3.60.2")'
-RUN Rscript -e 'remotes::install_version("Matrix",upgrade="never", version = "1.7.0")'
-RUN Rscript -e 'remotes::install_version("matrixcalc",upgrade="never", version = "1.0.6")'
-RUN Rscript -e 'remotes::install_github("Breeding-Insight/BIGr",upgrade="never")'
-RUN Rscript -e 'remotes::install_github("jendelman/GWASpoly",upgrade="never")'
+# syntax=docker/dockerfile:1.7
+# Buildx/Actions will pass BASE_IMAGE as a manifest tag that covers both arches
+ARG BASE_IMAGE=docker.io/breedinginsight/bigapp-deps:r4.5-bioc3.21-2025-08
+FROM ${BASE_IMAGE}
 
-RUN mkdir /build_zone
-ADD . /build_zone
-WORKDIR /build_zone
-RUN R -e 'remotes::install_local(upgrade="never")'
-RUN rm -rf /build_zone
-EXPOSE 80
-CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');BIGapp::run_app()"
+SHELL ["/bin/bash","-eo","pipefail","-c"]
+ENV DEBIAN_FRONTEND=noninteractive TZ=UTC
+ENV MAKEFLAGS="-j2" R_PKG_INSTALL_ARGS="--no-build-vignettes --no-manual"
+
+# App install (only your code changes should rebuild this layer)
+WORKDIR /app
+COPY DESCRIPTION /app/
+# COPY NAMESPACE /app/  # if present, include for better cache hits
+COPY . /app
+RUN R -q -e "remotes::install_local('.', upgrade='never', dependencies=TRUE, \
+                                    INSTALL_opts=c('--no-build-vignettes','--no-manual'))"
 
+# Runtime
+RUN useradd -m appuser
+USER appuser
+WORKDIR /app
+EXPOSE 80
+HEALTHCHECK --interval=30s --timeout=5s --retries=5 \
+  CMD wget -qO- http://localhost:${PORT:-80}/ || exit 1
+CMD ["R","-q","-e","options(shiny.port=as.integer(Sys.getenv('PORT','80')), shiny.host='0.0.0.0'); BIGapp::run_app()"]

NAMESPACE

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,vcf_sanity_check)
 export(run_app)
+export(vcf_sanity_check)
+export(vcf_sanity_messages)
 import(BIGr)
 import(GWASpoly)
 import(dplyr)