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
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