[Bioc-devel] EXTERNAL: Re: Best practice use pkgdown, docker with Bioconductor

Marcel Ramos m@rce|@r@mo@perez @end|ng |rom ro@we||p@rk@org
Tue Apr 6 23:44:56 CEST 2021

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.



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 using v1
>          with:
>            username: ${{ secrets.DOCKER_USERNAME }}
>            password: ${{ secrets.DOCKER_TOKEN }}
>            repository: your/docker/path
>            tag_with_ref: true
>            tag_with_sha: true
>            tags: latest
> [https://avatars.githubusercontent.com/u/5640707?s=400&v=4]<https://github.com/jianhong/HMMtBroadPeak/tree/staging>
> jianhong/HMMtBroadPeak<https://github.com/jianhong/HMMtBroadPeak/tree/staging>
> call broad peak by a modified Baum_Welch algorithm that supports multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
> github.com
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Murphy, Alan E <a.murphy using imperial.ac.uk>
> Sent: Tuesday, April 6, 2021 10:24 AM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
> Hi all,
> I'm working on the development of (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$ ] 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
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Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

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