remove shopt dependency
diff --git a/pge/src/main/resources/config/PgeConfig_MimePartitioner.xml b/pge/src/main/resources/config/PgeConfig_MimePartitioner.xml
index b1454ac..ce9d8a1 100644
--- a/pge/src/main/resources/config/PgeConfig_MimePartitioner.xml
+++ b/pge/src/main/resources/config/PgeConfig_MimePartitioner.xml
@@ -5,7 +5,6 @@
   <!-- How to run the PGE -->
   <exe dir="[JobDir]" shell="/bin/bash">
      <cmd>export PATH=$HOME/bin/:${PATH}</cmd>
-     <cmd>shopt -s expand_aliases</cmd>
      <cmd>echo "Creating working dirs"</cmd>
      <cmd>mkdir [JobInputDir] ; mkdir [JobOutputDir]; mkdir [JobLogDir]</cmd>
      <cmd>echo "Running MIME partitioner"</cmd>
diff --git a/pge/src/main/resources/config/PgeConfig_Rat.xml b/pge/src/main/resources/config/PgeConfig_Rat.xml
index 12de6b9..41f7755 100644
--- a/pge/src/main/resources/config/PgeConfig_Rat.xml
+++ b/pge/src/main/resources/config/PgeConfig_Rat.xml
@@ -10,8 +10,7 @@
   <!-- How to run the PGE -->
   <exe dir="[JobDir]" shell="/bin/bash">
      <cmd>export PATH=$HOME/bin/:${PATH}</cmd>
-     <cmd>shopt -s expand_aliases</cmd>
-     <cmd>alias rat="java -jar [DRAT_HOME]/rat/lib/apache-rat-0.13.jar"</cmd>
+     <cmd>rat() { java -jar [DRAT_HOME]/rat/lib/apache-rat-0.13.jar $1; }</cmd>
      <cmd>echo "Creating working dirs"</cmd>
      <cmd>mkdir -p [JobInputDir] ; mkdir -p [JobOutputDir]; mkdir -p [JobLogDir]</cmd>
      <!-- <cmd>echo "Staging input to [JobInputDir]"</cmd>
diff --git a/pge/src/main/resources/config/PgeConfig_RatAggregator.xml b/pge/src/main/resources/config/PgeConfig_RatAggregator.xml
index 1cda5d0..fd99b1a 100644
--- a/pge/src/main/resources/config/PgeConfig_RatAggregator.xml
+++ b/pge/src/main/resources/config/PgeConfig_RatAggregator.xml
@@ -5,8 +5,7 @@
   <!-- How to run the PGE -->
   <exe dir="[JobDir]" shell="/bin/bash">
      <cmd>export PATH=$HOME/bin/:${PATH}</cmd>
-     <cmd>shopt -s expand_aliases</cmd>
-      <cmd>echo "Creating working dirs"</cmd>
+     <cmd>echo "Creating working dirs"</cmd>
      <cmd>mkdir [JobInputDir] ; mkdir [JobOutputDir]; mkdir [JobLogDir]</cmd>
      <cmd>echo "Running RAT aggregator"</cmd>
      <cmd>[RatAggregatorScript] `python -c "print ' '.join('[InputFiles]'.split(','))"` > [JobOutputDir]/rat_aggregate_stats_[DateMilis].csv</cmd>