From 54a37edf95993fa45f29c2827badee1185c7dab4 Mon Sep 17 00:00:00 2001 From: Johannes Rainer Date: Sun, 13 Oct 2024 08:13:47 +0200 Subject: [PATCH] Save results to shared folder --- Dockerfile | 4 ++++ vignettes/a-end-to-end-untargeted-metabolomics.qmd | 2 +- vignettes/alignment-to-external-dataset.qmd | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9752c47..f2c578c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,6 +25,10 @@ RUN Rscript -e "BiocManager::install(c('RCurl', 'xcms', 'MsExperiment', 'Summari ## Install the current package with vignettes RUN Rscript -e "devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = TRUE)" +## Create a directory we can use to share data. +RUN mkdir -p /shared/data; \ + chmod 777 /shared/data; + USER rstudio ## build article for end-to-end:test diff --git a/vignettes/a-end-to-end-untargeted-metabolomics.qmd b/vignettes/a-end-to-end-untargeted-metabolomics.qmd index 3ecfbd4..e20d22b 100644 --- a/vignettes/a-end-to-end-untargeted-metabolomics.qmd +++ b/vignettes/a-end-to-end-untargeted-metabolomics.qmd @@ -1713,7 +1713,7 @@ Javascript as well as loaded easily back into R. # 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 = "/tmp/preprocessed_lcms1.RData") +save(lcms1, file = "/shared/data/preprocessed_lcms1.RData") ``` # Data normalization diff --git a/vignettes/alignment-to-external-dataset.qmd b/vignettes/alignment-to-external-dataset.qmd index 57b17f0..3c2bdb4 100644 --- a/vignettes/alignment-to-external-dataset.qmd +++ b/vignettes/alignment-to-external-dataset.qmd @@ -77,7 +77,7 @@ tmp <- readMsObject(MsExperiment(), ``` ```{r} -load("/tmp/preprocessed_lcms1.RData") +load("/shared/data/preprocessed_lcms1.RData") ``` ## Load unprocessed LC-MS/MS data