diff --git a/tools/ngs_rna/cuffcompare_wrapper.xml b/tools/ngs_rna/cuffcompare_wrapper.xml
index 11e0ca75f0d..9c3124e64fb 100644
--- a/tools/ngs_rna/cuffcompare_wrapper.xml
+++ b/tools/ngs_rna/cuffcompare_wrapper.xml
@@ -4,6 +4,7 @@
     <requirements>
         <requirement type="package">cufflinks</requirement>
     </requirements>
+    <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command>
     <command interpreter="python">
         cuffcompare_wrapper.py 
             
diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 0aed5f372bd..3f7b3b7513b 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -4,6 +4,7 @@
     <requirements>
         <requirement type="package">cufflinks</requirement>
     </requirements>
+    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
     <command>
         cuffdiff
             --FDR=$fdr
diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 6f002c6626e..d03180338c4 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -4,6 +4,7 @@
     <requirements>
         <requirement type="package">cufflinks</requirement>
     </requirements>
+    <version_command>cufflinks 2>&amp;1 | head -n 1</version_command>
     <command interpreter="python">
         cufflinks_wrapper.py 
             --input=$input