[Bioc-devel] Add dockerhub push to github repository

[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.
________________________________
From: Nuno Agostinho <nunodanielagostinho using gmail.com>
Sent: 03 June 2021 11:57
To: Murphy, Alan E <a.murphy using imperial.ac.uk>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Add dockerhub push to github repository


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Hey Alan,

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?

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

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 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?

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 using v2
      with:
        push: true
        tags: ${{ github.repository }}:${{ env.packageVersion }}

Is there a way to tell the Dockerfile to install the R package in the current repository?

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

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

Best,
Nuno Agostinho

On 3 Jun 2021, at 07:52, Murphy, Alan E <a.murphy using imperial.ac.uk<mailto:a.murphy using imperial.ac.uk>> wrote:

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

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