Merge pull request #61 from MHH-RCUG/dev

Uncomment temp directory code, solves container download problems
MHH-RCUG · Nov 10, 2020 · b498f6b · b498f6b
2 parents dd0d425 + 2146713
commit b498f6b
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Showing 3 changed files with 13 additions and 8 deletions.
diff --git a/scrnaseq_app.R b/scrnaseq_app.R
@@ -461,9 +461,9 @@ server = function(input, output, session) {
       paste0(input$archive_download, ".zip")
     },
     content = function(file) {
-      # temporarily switch to the temp dir, in case you do not have write permission to the current working directory
-      # owd = setwd(tempdir())
-      # on.exit(setwd(owd))
+       #temporarily switch to the temp dir, in case you do not have write permission to the current working directory
+       owd = setwd(tempdir())
+       on.exit(setwd(owd))
 
       # Idea to check if all devices are off on exit
       # on.exit({

diff --git a/singularity/README.md b/singularity/README.md
@@ -38,7 +38,7 @@ ps -aux | grep R
 kill <PID> 
 
 # Start container
-singularity exec ../../scrnaseq_app.simg     R -e "options('shiny.port'=3838,shiny.host='0.0.0.0'); shiny::runApp('/data/scrnaseq_app/scrnaseq_app.R')"
+singularity exec  ../../scrnaseq_app.simg     R -e "options('shiny.port'=3838,shiny.host='0.0.0.0'); shiny::runApp('/data/scrnaseq_app/scrnaseq_app.R')"
 ```
 
 
@@ -56,8 +56,13 @@ singularity version
 https://njstem.wordpress.com/2018/08/02/r-script-seurat-with-a-singularity-container-using-slurm/
 
 
-### Dependencies : downloaded in script
+### Dependencies : was previously downloaded in script
 ```
 git clone https://github.com/MHH-RCUG/scrnaseq_app
 wget https://owncloud.gwdg.de/index.php/s/rRawkhIOVe1T5qi/download
 ```
+
+
+### Writable containers
+-Just for sandbox directories for testing
+-Instead, write images to directories which are bound into the container, eg /home/$USER, or /tmp
diff --git a/singularity/singularity_app_recipe.txt b/singularity/singularity_app_recipe.txt
@@ -111,9 +111,9 @@ MirrorURL: http://de.archive.ubuntu.com/ubuntu/
     #git checkout marius_changes
 
 
-    # download required example file
-    wget https://owncloud.gwdg.de/index.php/s/rRawkhIOVe1T5qi/download
-    mv download pbmc_2020-06-08.rds
+    # download required example file 
+    #wget https://owncloud.gwdg.de/index.php/s/rRawkhIOVe1T5qi/download
+    #mv download pbmc_2020-06-08.rds