Save results to shared folder

rformassspectrometry · Oct 13, 2024 · 54a37ed · 54a37ed
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand Down @@