Fix submission script syntax

Control/CalypsoExample/Digitization/scripts/submit_faserMDC_digi.sh

@@ -186,7 +186,7 @@ then
     ls -l
     echo "copy *-RDO.root to $outdest"
     mkdir -p $outdest
-    eos cp *-RDO.root $outdest
+    eos cp *-RDO.root ${outdest}/ || true
 fi
 #
 # Also copy log file
@@ -196,12 +196,12 @@ then
     ls -l
     echo "copy $logfile to $logdest"
     mkdir -p $logdest
-    eos cp $logfile $logdest
+    eos cp $logfile $logdest/$logfile
 elif ! [ -z "$outdest" ]
 then 
     cd ..
     ls -l
     echo "copy $logfile to $outdest"
     mkdir -p $outdest
-    eos cp $logfile $outdest
+    eos cp $logfile $outdest/$logfile
 fi

Control/CalypsoExample/Digitization/scripts/submit_faserMDC_digi_merge.sh

@@ -209,7 +209,7 @@ then
     ls -l
     echo "copy *-RDO.root to $outdest"
     mkdir -p $outdest
-    eos cp *-RDO.root $outdest
+    eos cp *-RDO.root ${outdest}/ || true
 fi
 #
 # Also copy log file
@@ -219,12 +219,12 @@ then
     ls -l
     echo "copy $logfile to $logdest"
     mkdir -p $logdest
-    eos cp $logfile $logdest
+    eos cp $logfile $logdest/$logfile
 elif ! [ -z "$outdest" ]
 then 
     cd ..
     ls -l
     echo "copy $logfile to $outdest"
     mkdir -p $outdest
-    eos cp $logfile $outdest
+    eos cp $logfile $outdest/$logfile
 fi

Control/CalypsoExample/Reconstruction/scripts/submit_faserMDC_reco.sh

@@ -175,7 +175,8 @@ then
     ls -l
     echo "copy *-RDO.root to $outdest"
     mkdir -p $outdest
-    eos cp *-xAOD.root $outdest
+    # Keep this line from stopping script, so we might get a log file
+    eos cp *-xAOD.root ${outdest}/ || true
 fi
 #
 # Also copy log file
@@ -185,12 +186,12 @@ then
     ls -l
     echo "copy $logfile to $logdest"
     mkdir -p $logdest
-    eos cp $logfile $logdest
+    eos cp $logfile $logdest/$logfile
 elif ! [ -z "$outdest" ]
 then 
     cd ..
     ls -l
     echo "copy $logfile to $outdest"
     mkdir -p $outdest
-    eos cp $logfile\ $outdest
+    eos cp $logfile $outdest/$logfile
 fi

Control/CalypsoExample/Reconstruction/scripts/submit_faser_reco.sh

@@ -156,11 +156,11 @@ else
 fi
 cd "$file_stem"
 #
-# Run job, || True ensures script continues even if job fails
+# Run job
 if [[ -z "$tag" ]]; then
-    faser_reco.py "--nevents=$nevents" "$file_path" || True
+    faser_reco.py "--nevents=$nevents" "$file_path" 
 else
-    faser_reco.py "--nevents=$nevents" "--reco=$tag" "$file_path" || True
+    faser_reco.py "--nevents=$nevents" "--reco=$tag" "$file_path" 
 fi
 #
 # Print out ending time
@@ -176,7 +176,9 @@ then
     ls -l
     echo "copy *-RDO.root to $outdest"
     mkdir -p $outdest
-    eos cp *-xAOD.root $outdest || True
+    # Keep this line from stopping script, so we might get a log file
+    # || true ensures script continues even if copy fails
+    eos cp *-xAOD.root ${outdest}/ || true   
 fi
 #
 # Copy log file second
@@ -186,12 +188,12 @@ then
     ls -l
     echo "copy $logfile to $logdest"
     mkdir -p $logdest
-    eos cp $logfile $logdest
+    eos cp $logfile $logdest/$logfile
 elif ! [ -z "$outdest" ]
 then 
     cd ..
     ls -l
     echo "copy $logfile to $outdest"
     mkdir -p $outdest
-    eos cp $logfile\ $outdest
+    eos cp $logfile $outdest/$logfile
 fi

Control/CalypsoExample/Simulation/scripts/submit_faserMDC_simulate.sh

@@ -199,7 +199,7 @@ then
     ls -l
     echo "copy *-HITS.root to $outdest"
     mkdir -p $outdest
-    eos cp *-HITS.root $outdest
+    eos cp *-HITS.root ${outdest}/ || true
 fi
 #
 # Also copy log file
@@ -209,13 +209,13 @@ then
     ls -l
     echo "copy $logfile to $logdest"
     mkdir -p $logdest
-    eos cp $logfile $logdest
+    eos cp $logfile $logdest/$logfile
 elif ! [ -z "$outdest" ]
 then 
     cd ..
     ls -l
     echo "copy $logfile to $outdest"
     mkdir -p $outdest
-    eos cp $logfile $outdest
+    eos cp $logfile $outdest/$logfile
 fi