Thank you Jianhong for the clean solution. I would encourage Alan to check out the biocthis::use_bioc_github_action to set up the Docker build and pkgdown.
Best, Marcel On 4/6/21 12:48 PM, Jianhong Ou, Ph.D. wrote: > Hi Alan, > > Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. > Hope this help. > > You may want to add one more step after check and before pkgdown to push to > your dockerhub by: > > - name: push to docker > - uses: docker/build-push-action@v1 > with: > username: ${{ secrets.DOCKER_USERNAME }} > password: ${{ secrets.DOCKER_TOKEN }} > repository: your/docker/path > tag_with_ref: true > tag_with_sha: true > tags: latest > [https://avatars.githubusercontent.com/u/5640707?s=400&v=4]<https://github.com/jianhong/HMMtBroadPeak/tree/staging> > jianhong/HMMtBroadPeak<https://github.com/jianhong/HMMtBroadPeak/tree/staging> > call broad peak by a modified Baum_Welch algorithm that supports > multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak > github.com > > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Murphy, Alan > E <a.mur...@imperial.ac.uk> > Sent: Tuesday, April 6, 2021 10:24 AM > To: bioc-devel@r-project.org <bioc-devel@r-project.org> > Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor > > Hi all, > > I'm working on the development of > (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$ > ] and have a question regarding a reviewer note. My package currently uses > pkgdown to create a website through the master branch. I also create and push > a new docker image from the main branch when the package successfully builds > on travis. > > My reviewer has asked to remove the related files > _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any > issues with these external configurations and Bioconductor. My reviewer has > suggested to put these in another branch. It's not clear to me how best to do > this? Ideally, if they are in a separate branch, is there a way to run them > once there is an update and successful build on the master branch? If this > isn't possible, is there a way to avoid manually duplicating new changes in > the master branch in this separate branch and instead, just push the changes > from master to this separate branch and trigger pkgdown and docker build that > way? Sorry, I realise this last part more so relates to github commands but I > was thinking someone else has probably already foudn a way around this issue. > > Kind regards, > Alan. > > Alan Murphy > Bioinformatician > Neurogenomics lab > UK Dementia Research Institute > Imperial College London > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPX4panddY$ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
