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Merge pull request #36 from CCBR/dockers
feat: docker files build
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‎.github/workflows/docker.yaml

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name: Build and push Docker images
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on:
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push:
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branches:
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- 'main'
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- 'docker'
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jobs:
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generate-matrix:
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runs-on: ubuntu-latest
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outputs:
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matrix-metadata: ${{ steps.metadata.outputs.matrix }}
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steps:
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- uses: hellofresh/action-changed-files@v3
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id: metadata
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with:
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pattern: docker/(?P<image_dir>\w+)/.*
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default-patterns: |
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meta.yml
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Dockerfile
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update-docker:
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needs: [generate-matrix]
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strategy:
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matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
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if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: pietrobolcato/[email protected]
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id: metadata
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with:
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config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
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- name: Get date
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id: date
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run: |
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echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
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- name: Login to DockerHub
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#if: github.event_name != 'pull_request'
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Build and push
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uses: docker/build-push-action@v4
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# only try building & pushing the container if parsing the metadata worked
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if: ${{ steps.metadata.outputs['container'] != '' }}
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with:
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context: docker/${{ matrix.image_dir }}
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# only push container to docker hub if not triggered from a PR
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.metadata.outputs['container'] }}
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build-args: |
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BUILD_DATE=${{ steps.date.outputs.DATE }}
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BUILD_TAG=${{ steps.metadata.outputs['version'] }}
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REPONAME=${{ steps.metadata.outputs['image_name'] }}

‎docker/annotate_cnvsv/Dockerfile

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FROM --platform=linux/amd64 nciccbr/ccbr_ubuntu_base_20.04:v5
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# build time variables
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ARG BUILD_DATE="000000"
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ENV BUILD_DATE=${BUILD_DATE}
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ARG BUILD_TAG="000000"
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ENV BUILD_TAG=${BUILD_TAG}
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ARG REPONAME="000000"
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ENV REPONAME=${REPONAME}
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LABEL maintainer <[email protected]>
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# Create Container filesystem specific
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# working directory and opt directories
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WORKDIR /opt2
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###Create AnnotSV
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RUN wget https://github.com/lgmgeo/AnnotSV/archive/refs/tags/v3.3.6.tar.gz \
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&& tar -xvjf /opt2/3.3.6.tar.gz \
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&& rm /opt2/3.3.6.tar.gz
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ENV PATH="/opt2/AnnotSV-3.3.6/bin:$PATH"
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##ClassifyCNV
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##Update the resources for ClassifyCNV
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RUN wget https://github.com/Genotek/ClassifyCNV/archive/refs/tags/v1.1.1.tar.gz \
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&& tar -xvjf /opt2/v1.1.1.tar.gz \
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&& rm /opt2/v1.1.1.tar.gz
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ENV PATH="/opt2/ClassifyCNV-1.1.1:$PATH"
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RUN update_clingen.sh
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COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
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RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
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‎docker/annotate_cnvsv/meta.yml

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dockerhub_namespace: dnousome
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image_name: ccbr_annotate_cnvsv
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version: v0.0.1
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container: "$(dockerhub_namespace)/$(image_name):$(version)"

‎docker/lofreq/Dockerfile

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FROM --platform=linux/amd64 ubuntu:22.04
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# build time variables
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ARG BUILD_DATE="000000"
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ENV BUILD_DATE=${BUILD_DATE}
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ARG BUILD_TAG="000000"
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ENV BUILD_TAG=${BUILD_TAG}
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ARG REPONAME="000000"
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ENV REPONAME=${REPONAME}
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LABEL maintainer <[email protected]>
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# Create Container filesystem specific
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# working directory and opt directories
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# This section installs system packages required for your project
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# If you need extra system packages add them here.
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RUN apt-get update \
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&& apt-get -y upgrade \
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&& DEBIAN_FRONTEND=noninteractive apt-get install -y \
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automake \
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build-essential \
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curl \
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git \
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gcc \
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libbz2-dev \
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libcurl4-gnutls-dev \
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libgsl0-dev \
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libperl-dev \
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liblzma-dev \
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libncurses5-dev \
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libssl-dev \
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python3-dev \
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zlib1g-dev
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RUN ln -s /usr/bin/python3.10 /usr/bin/python
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WORKDIR /opt2
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ARG htsversion=1.19
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RUN curl -L https://github.com/samtools/htslib/releases/download/${htsversion}/htslib-${htsversion}.tar.bz2 | tar xj \
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&& cd htslib-${htsversion} \
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&& ./configure \
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&& make \
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&& make install
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RUN curl -L https://github.com/samtools/bcftools/releases/download/${htsversion}/bcftools-${htsversion}.tar.bz2 | tar xj \
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&& cd bcftools-${htsversion} \
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&& ./configure && make && make install
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RUN git clone https://github.com/CSB5/lofreq \
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&& cd lofreq \
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&& ./bootstrap \
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&& ./configure --with-htslib=/usr/local \
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&& make \
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&& make install
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ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH

‎docker/lofreq/build.sh

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# Build image
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docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.4 -f Dockerfile .
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docker tag ccbr_lofreq:v0.0.1 dnousome/ccbr_lofreq:v0.0.1
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docker push dnousome/ccbr_lofreq:v0.0.1
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docker push dnousome/ccbr_logan_base:latest
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‎docker/logan_base/meta.yml

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dockerhub_namespace: dnousome
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image_name: ccbr_logan_base
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version: v0.3.4
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container: "$(dockerhub_namespace)/$(image_name):$(version)"

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