diff --git a/Dockerfile b/Dockerfile index 0896f71..152d6be 100644 --- a/Dockerfile +++ b/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 {} + diff --git a/vignettes/a-end-to-end-untargeted-metabolomics.qmd b/vignettes/a-end-to-end-untargeted-metabolomics.qmd index e20d22b..5fa0065 100644 --- a/vignettes/a-end-to-end-untargeted-metabolomics.qmd +++ b/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