Copy preprocessed data to /shared/data/

Dockerfile

@@ -15,8 +15,7 @@ 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; \
-    chmod 777 /shared/data;
+RUN mkdir -p /shared/data
 
 ## Install the required packages
 RUN Rscript -e "BiocManager::install(c('RCurl', 'xcms', 'MsExperiment', 'SummarizedExperiment', \
@@ -36,4 +35,8 @@ RUN Rscript -e "quarto::quarto_render('vignettes/a-end-to-end-untargeted-metabol
 
 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 find vignettes/ -name "*.html" -type f -delete && find vignettes/ -name "*_files" -type d -exec rm -r {} +

vignettes/a-end-to-end-untargeted-metabolomics.qmd

@@ -1710,10 +1710,10 @@ Javascript as well as loaded easily back into R.
 
 ```{r}
 #' Save the preprocessing results
-# d <- file.path(tempdir(), "objects/lcms1")
+#' d <- file.path(tempdir(), "objects/lcms1")
 # saveMsObject(lcms1, AlabasterParam(path = d))
-#for now let's do R object because the previous method is not implemented yet.
-save(lcms1, file = "/shared/data/preprocessed_lcms1.RData")
+#' for now let's do R object because the previous method is not implemented yet.
+save(lcms1, file = "preprocessed_lcms1.RData")
 ```
 
 # Data normalization