star debugging

dge_workflow/star_align.sh

@@ -52,7 +52,7 @@ fi
 
 ## build index if not present
 if [ ! -f "${star_index}/SA" ]; then
-chmod -R +w ${star_index}
+chmod +w $(dirname ${star_index})
 
 mailme "${project}: creating STAR index for $igenome"
 mkdir ${star_index}
@@ -63,7 +63,7 @@ cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles
 mysub "${project}_star_index" "$cmd" -n 5 -R span[hosts=1] -q medium  | blockScript
 
 ## prevent modification
-chmod -R -w ${star_index}
+chmod -w $(dirname ${star_index})
 fi