diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index aaf29cac3bc..cd4d0533a98 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -326,6 +326,7 @@
   <section name="NGS: RNA Analysis" id="ngs-rna-tools">
    <label text="RNA-seq" id="rna_seq" />
       <tool file="ngs_rna/tophat_wrapper.xml" />
+      <tool file="ngs_rna/tophat2_wrapper.xml" />
       <tool file="ngs_rna/cufflinks_wrapper.xml" />
       <tool file="ngs_rna/cuffcompare_wrapper.xml" />
  	    <tool file="ngs_rna/cuffmerge_wrapper.xml" />
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 56fdf30e359..a8961fe98a4 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -3,6 +3,8 @@
     <description>Find splice junctions using RNA-seq data</description>
     <version_command>tophat --version</version_command>
     <requirements>
+        <requirement type="package">samtools</requirement>
+        <requirement type="package">bowtie</requirement>
         <requirement type="package">tophat</requirement>
     </requirements>
     <command interpreter="python">