feat: docker files build

.github/workflows/docker.yaml

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+name: Build and push Docker images   
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'docker'
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix-metadata: ${{ steps.metadata.outputs.matrix }}
+    steps:
+      - uses: hellofresh/action-changed-files@v3
+        id: metadata
+        with:
+          pattern: docker/(?P<image_dir>\w+)/.*
+          default-patterns: |
+            meta.yml
+            Dockerfile
+      
+  update-docker:
+    needs: [generate-matrix]
+    strategy:
+      matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
+    if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/action-read-yaml@1.0.0
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
+      - name: Get date
+        id: date
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
+      - name: Login to DockerHub
+        #if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: docker/${{ matrix.image_dir }}
+          # only push container to docker hub if not triggered from a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.date.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}

docker/annotate_cnvsv/Dockerfile

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

docker/annotate_cnvsv/meta.yml

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

docker/lofreq/Dockerfile

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

docker/lofreq/build.sh

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

docker/logan_base/meta.yml

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