diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.py b/lib/galaxy/datatypes/converters/sam_to_bam.py
index dcc84b6c518..011f660b922 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam.py
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.py
@@ -34,18 +34,17 @@ def _get_samtools_version():
     if not cmd_exists('samtools'):
         raise Exception('This tool needs samtools, but it is not on PATH.')
     # Get the version of samtools via --version-only, if available
-    p = subprocess.Popen(['samtools', '--version-only'],
-                         stdout=subprocess.PIPE,
-                         stderr=subprocess.PIPE)
-    output, error = p.communicate()
-
-    # --version-only is available
-    # Format is <version x.y.z>+htslib-<a.b.c>
-    if p.returncode == 0:
+    try:
+        output = subprocess.check_output(['samtools', '--version-only'], stderr=subprocess.PIPE)
+        # --version-only is available
+        # Format is <version x.y.z>+htslib-<a.b.c>
         version = output.split('+')[0]
         return version
+    except subprocess.CalledProcessError:
+        # --version-only not available
+        pass
 
-    output = subprocess.Popen(['samtools'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[1]
+    output = subprocess.check_output(['samtools'], stderr=subprocess.PIPE)
     lines = output.split('\n')
     for line in lines:
         if line.lower().startswith('version'):