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ypriverolypriverol
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added new containers of DIANN
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‎.github/workflows/quantms-containers.yml‎

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@@ -122,6 +122,126 @@ jobs:
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run: |
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echo "::error::Failed to build or push DiaNN 2.1.0 images. Check the logs for details."
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build-diann-2-2-0:
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name: Build and Push DiaNN 2.2.0 Docker Images
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Build and Push DiaNN 2.2.0 image
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uses: docker/build-push-action@v5
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with:
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context: ./diann-2.2.0
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push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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tags: ghcr.io/bigbio/diann:2.2.0
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cache-from: type=gha
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cache-to: type=gha,mode=max
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provenance: false
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- name: Set up Singularity
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.7
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- name: Convert to Singularity and push
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if: (github.event_name != 'pull_request')
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run: |
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docker pull ghcr.io/bigbio/diann:2.2.0
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docker save ghcr.io/bigbio/diann:2.2.0 -o diann-2.2.0.tar
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singularity build diann-2.2.0.sif docker-archive://diann-2.2.0.tar
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echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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singularity push diann-2.2.0.sif oras://ghcr.io/bigbio/diann-sif:2.2.0
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build-diann-2-0:
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name: Build and Push DiaNN 2.0.2 Docker Images
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Build and Push DiaNN 2.0.2 image
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uses: docker/build-push-action@v5
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with:
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context: ./diann-2.0
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push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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tags: ghcr.io/bigbio/diann:2.0.2
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cache-from: type=gha
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cache-to: type=gha,mode=max
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provenance: false
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- name: Set up Singularity
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.7
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- name: Convert to Singularity and push
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if: (github.event_name != 'pull_request')
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run: |
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docker pull ghcr.io/bigbio/diann:2.0.2
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docker save ghcr.io/bigbio/diann:2.0.2 -o diann-2.0.2.tar
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singularity build diann-2.0.2.sif docker-archive://diann-2.0.2.tar
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echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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singularity push diann-2.0.2.sif oras://ghcr.io/bigbio/diann-sif:2.0.2
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build-diann-1-9-2:
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name: Build and Push DiaNN 1.9.2 Docker Images
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Build and Push DiaNN 1.9.2 image
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uses: docker/build-push-action@v5
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with:
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context: ./diann-1.9.2
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push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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tags: ghcr.io/bigbio/diann:1.9.2
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cache-from: type=gha
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cache-to: type=gha,mode=max
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provenance: false
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- name: Set up Singularity
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.7
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- name: Convert to Singularity and push
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if: (github.event_name != 'pull_request')
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run: |
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docker pull ghcr.io/bigbio/diann:1.9.2
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docker save ghcr.io/bigbio/diann:1.9.2 -o diann-1.9.2.tar
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singularity build diann-1.9.2.sif docker-archive://diann-1.9.2.tar
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echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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singularity push diann-1.9.2.sif oras://ghcr.io/bigbio/diann-sif:1.9.2
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build-diann-1-8-1:
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name: Build and Push DiaNN 1.8.1 Docker Images
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runs-on: ubuntu-latest
@@ -284,7 +404,7 @@ jobs:
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sync-openms:
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name: Sync OpenMS Containers
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needs: [build-diann-2-1-0, build-diann-1-8-1, build-relink-1-0-0]
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needs: [build-diann-2-2-0, build-diann-2-1-0, build-diann-2-0, build-diann-1-9-2, build-diann-1-8-1, build-relink-1-0-0]
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runs-on: ubuntu-latest
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permissions:
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contents: read

‎diann-1.9.2/Dockerfile‎

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FROM ubuntu:22.04
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LABEL base_image="ubuntu:22.04"
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LABEL version="1"
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LABEL software="diann"
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LABEL software.version="1.9.2"
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LABEL about.summary="DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing."
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LABEL about.home="https://github.com/vdemichev/DiaNN"
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LABEL about.documentation="https://github.com/vdemichev/DiaNN"
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LABEL about.license_file="https://github.com/vdemichev/DiaNN/LICENSE.txt"
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LABEL about.tags="Proteomics"
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LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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unzip \
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libgomp1 \
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locales && \
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rm -rf /var/lib/apt/lists/*
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RUN locale-gen en_US.UTF-8 && \
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update-locale LANG=en_US.UTF-8
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ENV LANG=en_US.UTF-8
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ENV LANGUAGE=en_US:en
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ENV LC_ALL=en_US.UTF-8
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# Download DIA-NN 1.9.2 (release tag: 1.9.2)
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RUN wget --no-check-certificate https://github.com/vdemichev/DiaNN/releases/download/1.9.2/diann-1.9.2.Linux.zip && \
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unzip diann-1.9.2.Linux.zip -d /usr/diann-1.9.2/ && \
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rm diann-1.9.2.Linux.zip
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RUN apt-get remove -y wget unzip && apt-get autoremove -y && apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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RUN chmod +x /usr/diann-1.9.2/diann-linux || chmod +x /usr/diann-1.9.2/diann
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RUN ln -sf /usr/diann-1.9.2/diann-linux /usr/diann-1.9.2/diann 2>/dev/null || true
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ENV PATH="$PATH:/usr/diann-1.9.2"
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WORKDIR /data/
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# NOTE: It is entirely the user's responsibility to ensure compliance with DIA-NN license terms.

‎diann-2.0/Dockerfile‎

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FROM ubuntu:22.04
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LABEL base_image="ubuntu:22.04"
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LABEL version="1"
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LABEL software="diann"
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LABEL software.version="2.0"
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LABEL about.summary="DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing."
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LABEL about.home="https://github.com/vdemichev/DiaNN"
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LABEL about.documentation="https://github.com/vdemichev/DiaNN"
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LABEL about.license_file="https://github.com/vdemichev/DiaNN/LICENSE.txt"
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LABEL about.tags="Proteomics"
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LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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unzip \
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libgomp1 \
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locales && \
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rm -rf /var/lib/apt/lists/*
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RUN locale-gen en_US.UTF-8 && \
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update-locale LANG=en_US.UTF-8
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ENV LANG=en_US.UTF-8
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ENV LANGUAGE=en_US:en
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ENV LC_ALL=en_US.UTF-8
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# Download DIA-NN 2.0.2 (latest 2.0.x patch, release tag: 2.0)
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RUN wget --no-check-certificate https://github.com/vdemichev/DiaNN/releases/download/2.0/DIA-NN-2.0.2-Academia-Linux.zip && \
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unzip DIA-NN-2.0.2-Academia-Linux.zip -d /usr/ && \
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rm DIA-NN-2.0.2-Academia-Linux.zip
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RUN apt-get remove -y wget unzip && apt-get autoremove -y && apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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RUN chmod +x /usr/diann-2.0.2/diann-linux || chmod +x /usr/diann-2.0.2/diann
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RUN ln -sf /usr/diann-2.0.2/diann-linux /usr/diann-2.0.2/diann 2>/dev/null || true
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ENV PATH="$PATH:/usr/diann-2.0.2"
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WORKDIR /data/
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# NOTE: It is entirely the user's responsibility to ensure compliance with DIA-NN license terms.

‎diann-2.2.0/Dockerfile‎

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FROM ubuntu:22.04
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LABEL base_image="ubuntu:22.04"
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LABEL version="1"
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LABEL software="diann"
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LABEL software.version="2.2.0"
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LABEL about.summary="DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing."
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LABEL about.home="https://github.com/vdemichev/DiaNN"
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LABEL about.documentation="https://github.com/vdemichev/DiaNN"
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LABEL about.license_file="https://github.com/vdemichev/DiaNN/LICENSE.txt"
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LABEL about.tags="Proteomics"
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LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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unzip \
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libgomp1 \
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locales && \
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rm -rf /var/lib/apt/lists/*
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RUN locale-gen en_US.UTF-8 && \
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update-locale LANG=en_US.UTF-8
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ENV LANG=en_US.UTF-8
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ENV LANGUAGE=en_US:en
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ENV LC_ALL=en_US.UTF-8
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# Download DIA-NN 2.2.0 (release tag: 2.0)
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RUN wget --no-check-certificate https://github.com/vdemichev/DiaNN/releases/download/2.0/DIA-NN-2.2.0-Academia-Linux.zip && \
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unzip DIA-NN-2.2.0-Academia-Linux.zip -d /usr/ && \
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rm DIA-NN-2.2.0-Academia-Linux.zip
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RUN apt-get remove -y wget unzip && apt-get autoremove -y && apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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RUN chmod +x /usr/diann-2.2.0/diann-linux || chmod +x /usr/diann-2.2.0/diann
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RUN ln -sf /usr/diann-2.2.0/diann-linux /usr/diann-2.2.0/diann 2>/dev/null || true
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ENV PATH="$PATH:/usr/diann-2.2.0"
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WORKDIR /data/
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# NOTE: It is entirely the user's responsibility to ensure compliance with DIA-NN license terms.

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