Merge branch 'master' of github.com:minoda-lab/universc

name: CI to Docker hub runners

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      -

        name: Login to DockerHub

        uses: docker/login-action@v1 

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

  build:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

  run:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Hello world 

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"

    - name: Diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls

name: CI to Docker hub

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      -

        name: Login to DockerHub

        uses: docker/login-action@v1 

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

  build:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

  push:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: true

name: Docker Compose Actions Workflow

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: Build the stack

        run: docker-compose up -d

      - name: Status

        run: echo "build complete" 

      - name: Build config

        run: pwd; ls ../*; ls ../../*

      - name: Paths

        run: which cellranger; echo $PATH

      - name: Call functions

        run: bash test/test_call.sh

      - name: Test docker container

        run: docker run --network container:webapp-frontend appropriate/curl -s --retry 10 --retry-connrefused http://localhost:5000/

name: Docker Compose Actions Workflow

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: Build the stack

        run: docker-compose up -d

      - name: Build Status

        run: echo "build complete" 

      - name: set up Cell Ranger

        run: echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections

        run: apt-get update \

             && apt-get upgrade -y \

             && apt-get install -y \

             apt-utils \

             clang-6.0 \

             cython \

             dialog \

             gcc-multilib \

             git \

             gzip \

             libbz2-dev \

             liblzma-dev \

             libcairo2-dev \

             libcurl4-openssl-dev \

             libgfortran-5-dev \

             libffi-dev \

             libhdf5-dev \

             libhts-dev \

             liblz4-dev \

             liblz4-tool \

             libncurses-dev \

             libopenblas-dev \

             libpixman-1-dev \

             libpng-dev \

             libsodium-dev \

             libssl-dev \

             libtiff5-dev \

             libtiff-tools \

             libxml2-dev \

             libxslt1-dev \

             libzmq3-dev \

             llvm \

             lzma-dev \

             python-cairo \

             python-h5py \

             python-matplotlib \

             python-nacl \

             python-numpy \

             python-pip \

             python-libxml2 \

             python-lz4 \

             python-redis \

             python-ruamel.yaml \

             python-sip \

             python-sqlite \

             python-tables \

             python-tk \

             samtools \

             tar \

             wget \

             zlib1g-dev

        run: pip install Cython==0.28.0

        run: pip install libtiff

        run: wget https://dl.google.com/go/go1.11.linux-amd64.tar.gz \

             && tar -xvf go1.11.linux-amd64.tar.gz \

             && mv go /usr/local

        GOROOT=/usr/local/go

        environment:

            - GOROOT=/usr/local/go

            - GOPATH=$HOME/go

            -  PATH=$GOPATH/bin:$GOROOT/bin:$PATH

        run: ln -s /usr/lib/go-1.11/bin/go /usr/bin/go

        run: apt-get remove -y python-openssl \

             &&  apt-get install -y --reinstall python-openssl

        run: wget https://files.pythonhosted.org/packages/40/d0/8efd61531f338a89b4efa48fcf1972d870d2b67a7aea9dcf70783c8464dc/pyOpenSSL-19.0.0.tar.gz \

             && tar -xzvf pyOpenSSL-19.0.0.tar.gz \

             && cd pyOpenSSL-19.0.0 \ 

             python setup.py install \

             && cd ..

        run: git clone git@github.com:TomKellyGenetics/cellranger_clean.git \

             && cd cellranger_clean \

             && cp requirements.txt /opt/requirements.txt \

             && pip install --upgrade pip \

             && pip install -r /opt/requirements.txt \

             cd ..

        run: easy_install -U pip \

             && easy_install -U pyOpenSSL

        run: apt-get install python-dateutil

        run: apt-get install -y \

             curl \

             git  \

             && curl https://sh.rustup.rs -sSf | sh -s -- -y

        run: RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh  -s -- -y

        environment:

            - PATH=/root/.cargo/bin/:$PATH

            - PATH=$HOME/.cargo/bin:$PATH

        run: bash $HOME/.cargo/env

        run: rustup install 1.40.0

        run: rustup default 1.40.0

RUN mkdir -p cellranger-3.0.2.9001 \

  && cd cellranger-3.0.2.9001 \

  && mkdir -p cellranger-cs \

  && mkdir -p cellranger-cs/3.0.2.9001 \

  && cd /

# Build cellranger itself 

RUN git clone https://github.com/TomKellyGenetics/cellranger.git cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001  \

 && cd cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001 \

 && make && make louvain-clean &&  make louvain \

 && cd ../..

RUN ln -s /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/cellranger /cellranger-3.0.2.9001/cellranger \

 && cd /

COPY crconverter_open.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/bin/crconverter

COPY crconverter_open.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/bin/vlconverter

RUN gunzip -k /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz 

RUN curl -sL https://deb.nodesource.com/setup_13.x | bash - \

 && apt-get install -y nodejs

# Install Martian. Note that we're just building the executables, not the web stuff

RUN git clone --recursive https://github.com/martian-lang/martian.git \

 && cd martian \

 && make mrc mrf mrg mrp mrs mrstat mrjob

# Set up paths to cellranger. This is most of what sourceme.bash would do.

ENV PATH /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/:/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/bin:/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/bin/:/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/lib/bin:/martian/bin/:$PATH

ENV PYTHONPATH /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python:/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/lib/python:/martian/adapters/python:$PYTHONPATH

ENV MROPATH /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/mro/:/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/mro/

ENV _TENX_LD_LIBRARY_PATH whatever

# Install bcl2fastq. mkfastq requires it.

RUN apt-get update \

 && apt-get install -y alien unzip wget \

 && wget https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-19-1-linux.zip \

 && unzip bcl2fastq2*.zip \

 && alien bcl2fastq2*.rpm \

 && dpkg -i bcl2fastq2*.deb \

 && rm bcl2fastq2*.deb bcl2fastq2*.rpm bcl2fastq2*.zip

# Install STAR aligner

RUN wget https://github.com/alexdobin/STAR/archive/2.5.1b.tar.gz \

 && tar xf 2.5.1b.tar.gz \

 && rm 2.5.1b.tar.gz \

 && cd STAR-2.5.1b \

 && make \

 && mv bin/Linux_x86_64_static/STAR* /usr/bin \

 && cd .. \

 && rm -rf STAR-2.5.1b

# Install tsne python package. pip installing it doesn't work

RUN git clone https://github.com/TomKellyGenetics/tsne.git \

 && cd tsne \

 && make install \

 && python setup.py install \

 && cd .. \

 && rm -rf tsne

ENV PATH /cellranger-3.0.2.9001:$PATH

COPY run_tests.sh /run_tests.sh

      - name: Build config

        run: pwd; ls ../*; ls ../../*

      - name: Paths

        run: which cellranger; echo $PATH

      - name: Call functions

        run: bash test/test_call.sh

      - name: Test docker container

        run: docker run --network container:webapp-frontend appropriate/curl -s --retry 10 --retry-connrefused http://localhost:5000/

name: Test 10x Genomics

on: push

jobs:

  login:

    runs-on: ubuntu-20.04

    steps:

      -

        name: Login to DockerHub

        uses: docker/login-action@v1 

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

  test:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Run image

      run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest echo "hello from universc"

    - name: Call UniverSC

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

        run: bash /universc/test/test_call.sh

    - name: Run image

      run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest bash /universc/test/run_tests_10x.sh

    - name: Call UniverSC

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

        run: bash /universc/test/run_tests_10x.sh

  build:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: Build the stack

        run: docker-compose up -d

      - name: Status

        run: echo "build complete" 

      - name: Test runnning on 10x

        run:  test/run_tests_10x.sh