diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py
index 7ba9182948a..bdd8d3eebb4 100644
--- a/lib/galaxy/datatypes/images.py
+++ b/lib/galaxy/datatypes/images.py
@@ -18,7 +18,7 @@ class Image( data.Data ):
 class Gmaj( data.Data ):
     """Class describing a GMAJ Applet"""
     def set_peek( self, dataset ):
-        dataset.peek  = "<p align=\"center\"><applet code=\"edu.psu.bx.gmaj.MajApplet.class\" archive=\"static/gmaj/gmaj.jar\" width=\"200\" height=\"30\" align=\"middle\"> <param name=bundle value=\"display?id="+str(dataset.id)+"&tofile=yes&toext=.zip\"> <param name=buttonlabel value=\"Launch GMAJ\"><param name=nobutton value=\"false\"><param name=urlpause value=\"100\"><param name=debug value=\"false\"><i>Your browser is not responding to the &lt;applet&gt; tag.</i></applet></p>"
+        dataset.peek  = "<p align=\"center\"><applet code=\"edu.psu.bx.gmaj.MajApplet.class\" archive=\"/static/gmaj/gmaj.jar\" width=\"200\" height=\"30\" align=\"middle\"> <param name=bundle value=\"display?id="+str(dataset.id)+"&tofile=yes&toext=.zip\"> <param name=buttonlabel value=\"Launch GMAJ\"><param name=nobutton value=\"false\"><param name=urlpause value=\"100\"><param name=debug value=\"false\"><i>Your browser is not responding to the &lt;applet&gt; tag.</i></applet></p>"
         dataset.blurb = 'GMAJ Multiple Alignment Viewer'
         
     def display_peek(self, dataset):
diff --git a/static/gmaj/gmaj.jar b/static/gmaj/gmaj.jar
index e7fa6fa0b11..09f8c759fd5 100644
Binary files a/static/gmaj/gmaj.jar and b/static/gmaj/gmaj.jar differ
diff --git a/tools/visualization/GMAJ.py b/tools/visualization/GMAJ.py
index d770bd0f1a7..59406e93bcd 100644
--- a/tools/visualization/GMAJ.py
+++ b/tools/visualization/GMAJ.py
@@ -43,7 +43,7 @@ out_file = zipfile.ZipFile(out_file, "w") #, ZIP_DEFLATED)
 #determine organisms located in maf file.
 species = get_species_names( maf_file )
 
-GMAJ_str = "#:gmaj\n\ntitle = \"GMAJ through Galaxy\"\nalignfile = input.maf\n"
+GMAJ_str = "#:gmaj\n\ntitle = \"GMAJ through Galaxy\"\nalignfile = input.maf\nnowarn = bed_blocks bed_thick bed_name repeat_type_missing bed_name_prefix\ntabext = .%s\n" % (dbkey)
 if dbkey in species and len(species[dbkey])>0:
     GMAJ_str = GMAJ_str + "refseq = "+dbkey+"."+species[dbkey][0]+"\n"
 else:
diff --git a/tools/visualization/GMAJ.xml b/tools/visualization/GMAJ.xml
index 0bcb518004b..b27a8dde790 100644
--- a/tools/visualization/GMAJ.xml
+++ b/tools/visualization/GMAJ.xml
@@ -3,17 +3,17 @@
   <command interpreter="python2.4">GMAJ.py $out_file1 $maf_input $dbkey $exons_file $highlights_file $underlays_file $repeats_file $links_file</command>
   <inputs>
       <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
-      <param name="exons_file" type="data" format="txt" label="Exons File" optional="True"/>
-      <param name="highlights_file" type="data" format="txt" label="Highlights File" optional="True"/>
-      <param name="underlays_file" type="data" format="txt" label="Underlays File" optional="True"/>
-      <param name="repeats_file" type="data" format="txt" label="Repeats File" optional="True"/>
-      <param name="links_file" type="data" format="txt" label="Links File" optional="True"/>
+      <param name="exons_file" type="data" format="bed" label="Exons File" optional="True"/>
+      <param name="highlights_file" type="data" format="bed" label="Highlights File" optional="True"/>
+      <param name="underlays_file" type="data" format="bed" label="Underlays File" optional="True"/>
+      <param name="repeats_file" type="data" format="bed" label="Repeats File" optional="True"/>
+      <param name="links_file" type="data" format="bed" label="Links File" optional="True"/>
   </inputs>
   <outputs>
     <data name="out_file1" format="gmaj.zip"/>
   </outputs>
 <help>
-You can use this tool to view a set of MAF alignments.  You may also include optional additional information about the primary organism, please see the documentation for proper file formats.
+You can use this tool to view a set of MAF alignments.  You may also include optional additional information about the primary organism in the BED format.
 
 For detailed information on GMAJ, click here_.