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alex-sandercockalex-sandercock
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Merge pull request #145 from Breeding-Insight/development
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‎.github/workflows/dockerhub-on-version.yml‎

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

‎DESCRIPTION‎

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

‎Dockerfile‎

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

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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S3method(print,vcf_sanity_check)
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export(run_app)
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export(vcf_sanity_check)
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export(vcf_sanity_messages)
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import(BIGr)
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import(GWASpoly)
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import(dplyr)

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