Use Bioconductor RELEASE_3_19 docker image

jorainer · jorainer · commit 998baf8fa696 · 2024-05-13T12:25:38.000+02:00
diff --git 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
@@ -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
@@ -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
@@ -1,16 +1,16 @@
-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
 
 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
@@ -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
@@ -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")

Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@ jobs:`
`32`	`32`	`push: true`
`33`	`33`	`tag_with_ref: true`
`34`	`34`	`tag_with_sha: true`
`35`		`- tags: jorainer/xcms_tutorials:latest`
	`35`	`+ tags: jorainer/xcms_tutorials:RELEASE_3_19`
`36`	`36`	`-`
`37`	`37`	`name: Image digest`
`38`	`38`	`run: echo ${{ steps.docker_build.outputs.digest }}`