From 998baf8fa696b0102befcc03b4cf2cba09a7f8e7 Mon Sep 17 00:00:00 2001 From: jorainer Date: Mon, 13 May 2024 12:25:38 +0200 Subject: [PATCH] Use Bioconductor RELEASE_3_19 docker image --- .github/workflows/build_deploy.yaml | 2 +- .github/workflows/docker-push.yaml | 2 +- DESCRIPTION | 5 +++-- Dockerfile | 6 +++--- NEWS.md | 2 +- README.md | 17 ++++++++++------- 6 files changed, 19 insertions(+), 15 deletions(-) diff --git a/.github/workflows/build_deploy.yaml b/.github/workflows/build_deploy.yaml index 7212c08..aeb5124 100644 --- a/.github/workflows/build_deploy.yaml +++ b/.github/workflows/build_deploy.yaml @@ -7,7 +7,7 @@ on: jobs: build-and-deploy: runs-on: ubuntu-latest - container: jorainer/xcms_tutorials:latest + container: jorainer/xcms_tutorials:RELEASE_3_19 steps: ## Most of these steps are the same as the ones in ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml index 0f02eaa..9814951 100644 --- a/.github/workflows/docker-push.yaml +++ b/.github/workflows/docker-push.yaml @@ -32,7 +32,7 @@ jobs: push: true tag_with_ref: true tag_with_sha: true - tags: jorainer/xcms_tutorials:latest + tags: jorainer/xcms_tutorials:RELEASE_3_19 - name: Image digest run: echo ${{ steps.docker_build.outputs.digest }} diff --git a/DESCRIPTION b/DESCRIPTION index 8d77870..39faee5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,9 +36,10 @@ Suggests: rmarkdown, RColorBrewer, SummarizedExperiment, - pheatmap + pheatmap, + RCurl URL: https://jorainer.github.io/xcmsTutorials/ BugReports: https://github.com/jorainer/xcmsTutorials/issues/new VignetteBuilder: knitr RoxygenNote: 7.2.3 -DockerImage: jorainer/xcms_tutorials:latest +DockerImage: jorainer/xcms_tutorials:RELEASE_3_19 diff --git a/Dockerfile b/Dockerfile index d75e338..b70cf66 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,9 @@ -FROM bioconductor/bioconductor_docker:devel +FROM bioconductor/bioconductor_docker:RELEASE_3_19 LABEL name="jorainer/xcms_tutorials" \ url="https://github.com/jorainer/xcmsTutorials" \ maintainer="johannes.rainer@eurac.edu" \ - description="Docker container to run xcms tutorials." \ + description="Docker container to run xcms tutorials. This version bases on the Bioconductor release 3.19 docker image." \ license="Artistic-2.0" WORKDIR /home/rstudio @@ -11,6 +11,6 @@ WORKDIR /home/rstudio COPY --chown=rstudio:rstudio . /home/rstudio/ ## Install the xcmsTutorials package and additional required packages -RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE, type = 'source'); BiocManager::install(c('RCurl', 'xcms'), ask = FALSE, dependencies = TRUE, type = 'source'); BiocManager::install('sneumann/xcms')" +RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE, type = 'source'); BiocManager::install(c('RCurl', 'xcms'), ask = FALSE, dependencies = TRUE, type = 'source')" RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = TRUE, repos = BiocManager::repositories())" diff --git a/NEWS.md b/NEWS.md index d5e8acf..76ba7e2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## Changes in 1.1.0 -- Use Bioconductor 3.19 devel release. +- Use Bioconductor 3.19 release docker image and packages. - Add examples for simple quality assessment of BPC or BPS data. - Introduce parameter `ppm` for `PeakDensityParam` correspondence analysis method. diff --git a/README.md b/README.md index dbdd8f8..1643e50 100644 --- a/README.md +++ b/README.md @@ -49,21 +49,24 @@ The workshop files along with an R runtime environment including all required packages and the RStudio (Posit) editor are all bundled in a *docker* container. After installation, this docker container can be run on the computer and the code and examples from the workshop can be evaluated within this -environment (without the need to install any additional packages or files). The -required steps for installation are: +environment (without the need to install any additional packages or files). + +This version of the workshop uses packages from **Bioconductor release 3.19** +(May 2024) and hence bases on Bioconductor's docker container for that release +(*RELEASE_3_19*). The required steps for installation are: - If you don't already have, install [docker](https://www.docker.com/). Find installation information [here](https://docs.docker.com/desktop/). - Get the [docker image](https://hub.docker.com/r/jorainer/xcms_tutorials) of this tutorial e.g. from the command line with `docker pull - jorainer/xcms_tutorials:latest`. + jorainer/xcms_tutorials:RELEASE_3_19`. - Start the docker container, either through the Docker Desktop, or on the command line with ``` docker run \ -e PASSWORD=bioc \ -p 8787:8787 \ - jorainer/xcms_tutorials:latest + jorainer/xcms_tutorials:RELEASE_3_19 ``` - Enter `http://localhost:8787` in a web browser and log in with username @@ -72,9 +75,9 @@ required steps for installation are: the *vignettes* folder and evaluate the R code blocks in that document. -For manual installation, an R version >= 4.3.0 is required as well as recent -versions of the packages `MsExperiment`, `Spectra` and in particular the `xcms` -(version >= 4.1.0 is needed). These can be installed using the code below: +For manual installation, an R version >= 4.4.0 is required as well as recent +versions of the packages `MsExperiment`, `Spectra` and in particular the +`xcms`. These can be installed using the code below: ```r install.packages("BiocManager")