Merge pull request #9 from rformassspectrometry/phili

Phili

Dockerfile

@@ -14,26 +14,10 @@ COPY --chown=rstudio:rstudio . /home/rstudio/
 RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb
 RUN gdebi --non-interactive quarto-linux-amd64.deb
 
-## Create a directory we can use to share data.
-RUN mkdir -p /shared/data
-
 ## Install the required packages
 RUN Rscript -e "BiocManager::install(c('RforMassSpectrometry/MsIO', 'RforMassSpectrometry/MsBackendMetaboLights'), ask = FALSE, dependencies = TRUE)"
 
 ## Install the current package with vignettes
-RUN Rscript -e "devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = FALSE, repos = BiocManager::repositories())"
-
-USER rstudio
-
-## build article for end-to-end:test
-RUN Rscript -e "quarto::quarto_render('vignettes/a-end-to-end-untargeted-metabolomics.qmd', quiet = FALSE)"
-
-USER root
-
-## Copy the RData to the shared folder
-RUN cp /home/rstudio/vignettes/preprocessed_lcms1.RData /shared/data/
-RUN chmod -R 777 /shared
-
 RUN Rscript -e "devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = TRUE, repos = BiocManager::repositories())"
 
 RUN find vignettes/ -name "*.html" -type f -delete && find vignettes/ -name "*_files" -type d -exec rm -r {} +