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[Bioc-devel] Add dockerhub push to github repository

6 messages · Nuno Agostinho, Murphy, Alan E

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Murphy, Alan E
# 
Hi all,

I'm working on developing an R package with the aim to eventually submit to Bioconductor. I would like to automatically create a new image and push to dockerhub with github actions when I push changes to the github repository. Does anyone have an example of this process in their repositories?

Two things to also consider, I would ideally like the tag of this dockerhub push to be the R package version (from the DESCRIPTION) to differentiate between images, is this possible? Secondly, I currently have the dockerfile created but, since my R package repository is private I have been building the R package and using the tar.gz file in the dockerfile to install the package (rather than using devtools::install_github()). Is there a way to tell the Dockerfile to install the R package in the current repository?

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
Nuno Agostinho
# 
Hey Alan,
Well, I use GitHub actions to build a Docker image and push it to GitHub Container Registry, maybe this could help somehow: https://github.com/nuno-agostinho/psichomics/blob/master/.github/workflows/docker.yml <https://github.com/nuno-agostinho/psichomics/blob/master/.github/workflows/docker.yml>

I use GitHub releases to release a new package version and, every time I release a new version, a new Docker image is built (this image also gets automatically tagged with the latest tag). I also build Docker images every time I push changes to the dev branch.

Regarding DockerHub, I have DockerHub set up to automatically build Docker images every time I push to master (to create the latest tag) and dev branches in GitHub, as well as every time I create a new tag (which I do when creating new releases). I could put this in the GitHub actions, but I didn't bother yet.
I think you can run some bash script in your GitHub Actions based on your DESCRIPTION file. I would have to test but maybe something like:

    - name: Get R package version
      run: |
        version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
        echo "packageVersion=${version}" >> $GITHUB_ENV
      shell:
        bash {0}

You can then access this variable in other steps via ${{ env.packageVersion }} like so:

    - name: Build and push
      uses: docker/build-push-action at v2
      with:
        push: true
        tags: ${{ github.repository }}:${{ env.packageVersion }}
To build the image, I use ADD . . to put the GitHub repository content in the Docker image and then install the package using remotes::install_local(), as you can see from my Dockerfile: https://github.com/nuno-agostinho/psichomics/blob/master/Dockerfile <https://github.com/nuno-agostinho/psichomics/blob/master/Dockerfile>

I hope I was clear and helpful. Please tell me if you need help with anything else! :)

Best,
Nuno Agostinho

  
  


  


      

    

    

      
      

        


  

        

      Murphy, Alan E
    

    

      
      #
    

  


  

      
Hey Nuno,

Thank you very much for your comprehensive explanation!

I have a question regarding the `remotes::install_local()` approach in the dockerfile, is that installing the master branch or the current branch that has been pushed to? I ask as I'm working on 'dev-am' branch and I got the following error:

Building image [***/scfdev:combiz/scFlow:0.7.1 ***/scfdev:dev-am ***/scfdev:sha-658a6af]
invalid argument "***/scfdev:combiz/scFlow:0.7.1" for "-t, --tag" flag: invalid reference format
See 'docker build --help'.
Error: Error: exit status 125
Usage:
  github-actions build-push [flags]

Flags:
  -h, --help   help for build-push

exit status 125

Obviously, this may not be down to this but I'm just trying to rule things out since this was the only change I made to the dockerfile. The docker file has this added following your dockerfile:

## Install scFlow package
# Copy description
WORKDIR scFlow
ADD . .

# Install R package from source
RUN Rscript -e "remotes::install_local()"
RUN rm -rf *

Cheers,
Alan.

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Nuno Agostinho
    

    

      
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Hey Alan,

            

      
      
      
    

        
It is based on the current branch.

            

      
      
      
    

        
I don't think the problem is the Dockerfile, but the GitHub Actions workflow itself (specifically, the issue seems to be related with the tag of the image). Could you show me your GitHub Actions workflow file to check what is going on?

Cheers,
Nuno

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Murphy, Alan E
    

    

      
      #
    

  


  

      
Hey Nuno,

Thanks so much, see below.

Kind regards,
Alan.

name: R GitHub Actions

on:
  push:
    branches:
      - main
      - master
      - dev-am
  pull_request:
    branches:
      - main
      - master

jobs:
  R-CMD-check:
    name: R-CMD-check
    runs-on: ubuntu-latest
    container: almurphy/scfdev:latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RGL_USE_NULL: TRUE
    steps:
      - uses: actions/checkout at v2
      - name: Setup R
        uses: r-lib/actions/setup-r at v1
        with:
          install-r: false

      - name: Install dependencies
        run: |
          install.packages(c("remotes", "rcmdcheck"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
      - name: Check
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
        shell: Rscript {0}

      - name: Get R package version
        run: |
          version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
          echo "packageVersion=${version}" >> $GITHUB_ENV
        shell: bash {0}

      - name: Build and push
        uses: docker/build-push-action at v2
        with:
          push: true
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_TOKEN }}
          repository: almurphy/scfdev
          tag_with_ref: true
          tag_with_sha: true
          tags: ${{ github.repository }}:${{ env.packageVersion }}

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Nuno Agostinho
    

    

      
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Hey Alan,

I think the line "container: almurphy/scfdev:latest" should be removed, this should only be used if you want to run something within a container (in this case, you just want to create a container).

Also, you are using docker/build-push-action at v2 as if it was version 1, but they changed a lot this action in the new version, as you can see here: https://github.com/docker/build-push-action/blob/master/UPGRADE.md <https://github.com/docker/build-push-action/blob/master/UPGRADE.md>

I would remove the

            

      
      
      
    

        
and replace it with the following:

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action at v1

      - name: Login to DockerHub
        uses: docker/login-action at v1
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_TOKEN }}

      - name: Build and push
        uses: docker/build-push-action at v2
        with:
          push: true
          tags: ${{ github.repository}}:${{ env.packageVersion }}

Basically, the steps are more discrete now, tell me if it works and if you need help with anything else.

Cheers,
Nuno