diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 1d5a28f..a0b490f 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -34,7 +34,7 @@ jobs: run: | options(repos = c(CRAN = "https://cran.r-project.org")) BiocManager::repositories() - remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) + BiocManager::install("seandavi/BuildABiocWorkshop2020", dependencies = TRUE, update = TRUE, ask = FALSE) remotes::install_cran("rcmdcheck") shell: Rscript {0} diff --git a/Dockerfile b/Dockerfile index 29ea2fd..098f8c2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,4 +4,4 @@ WORKDIR /home/rstudio COPY --chown=rstudio:rstudio . /home/rstudio/ -RUN Rscript -e "devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" +RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install('seandavi/BuildABiocWorkshop2020', dependencies=TRUE, build_vignettes=TRUE, update = TRUE, ask = FALSE)" \ No newline at end of file diff --git a/vignettes/HOWTO_BUILD_WORKSHOP.Rmd b/vignettes/HOWTO_BUILD_WORKSHOP.Rmd index def2b96..e7c676c 100644 --- a/vignettes/HOWTO_BUILD_WORKSHOP.Rmd +++ b/vignettes/HOWTO_BUILD_WORKSHOP.Rmd @@ -50,6 +50,10 @@ desired Docker image name**. In other words, this section of the github actions file will build and push to dockerhub the image with this name. +**NOTE**: Dockerhub names must be all lowercase, can be two to 255 + characters, and can only contain lowercase letters, numbers or `-` and + `_` (https://docs.docker.com/docker-hub/repos/). + ```yaml - uses: docker/build-push-action@v1 @@ -64,6 +68,30 @@ this name. tags: latest ``` +Also change the repo name here (here it is case-insensitive): + +```yaml + - name: Install dependencies + run: | + options(repos = c(CRAN = "https://cran.r-project.org")) + BiocManager::repositories() + BiocManager::install("seandavi/BuildABiocWorkshop2020", dependencies = TRUE, update = TRUE, ask = FALSE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} +``` + +### Edit `Dockerfile` + +Change `seandavi/BuildABiocWorkshop2020` to the username/reponame of +your GitHub repo, to install your workshop and all its +Depends/Imports/Suggests and their dependencies into the Docker +container for your workshop. + +You can also choose to build on a different base Bioconductor Docker +image. For example, to build on release 3.11 instead of devel, change +`FROM bioconductor/bioconductor_docker:devel` to `FROM +bioconductor/bioconductor_docker:RELEASE_3_11`. + ### Add "secrets" to github repo Secrets are encrypted environment variables that you create in a