diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 3d6f6e0e1e4..724fcaf16e8 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@ import struct
 import subprocess
 import tempfile
 import re
+import warnings
 import zipfile
 
 from galaxy import eggs
@@ -24,8 +25,11 @@ from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListPa
 from galaxy.datatypes import metadata
 import dataproviders
 
-eggs.require( "pysam" )
-from pysam import csamtools
+with warnings.catch_warnings():
+    warnings.simplefilter( "ignore" )
+    eggs.require( "pysam" )
+    from pysam import csamtools
+
 
 log = logging.getLogger(__name__)