--- a/mirdeep2.xml	Tue Jan 27 09:06:24 2015 -0500
+++ b/mirdeep2.xml	Wed Feb 04 10:44:44 2015 -0500
@@ -60,20 +60,20 @@
     -b $min_score_cutoff
     $disable_randfold
     
-    ; cp result*.bed result.bed 2> /dev/null
-    ; cp result*.csv result.csv 2> /dev/null
-    ; cp mirdeep_runs/run*/output.mrd . 2> /dev/null
-    ; cp mirdeep_runs/run*/survey.csv . 2> /dev/null
+    ; mv result*.bed result.bed 2> /dev/null
+    ; mv result*.csv result.csv 2> /dev/null
+    ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
+    ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
     
     ## html output
     ;
-    cp result*.html $html 2> /dev/null
+    mv result*.html $html 2> /dev/null
     
     ## move pdf directory to be accessible from the new index.html
     ;
     mkdir -p $html.files_path 2> /dev/null
     ;
-    cp -R pdfs* $html.files_path 2> /dev/null
+    mv pdfs* $html.files_path 2> /dev/null
     
 ]]>
     </command>