diff --git a/chipathlon/jobs/params/music_punctate.yaml b/chipathlon/jobs/params/music_punctate.yaml
index 6b12172aeee599abda296b3154abec3d08f48f72..4e0bf45c828a93f1e959ec5aa3f1d2f091ae1b60 100644
--- a/chipathlon/jobs/params/music_punctate.yaml
+++ b/chipathlon/jobs/params/music_punctate.yaml
@@ -46,7 +46,7 @@ music_punctate:
     - name: scale_2216.bed
       type: file
       file_type: bed
-  command: run_music.py
+  command: music
   arguments:
     - "--prefix":
         type: string
diff --git a/chipathlon/jobs/scripts/run_music.py b/chipathlon/jobs/scripts/run_music.py
index 9180af18ca394b2798eed1c198a6e3744617937b..67c7603cb1d18928b3cccb1031738fd1efbbe687 100755
--- a/chipathlon/jobs/scripts/run_music.py
+++ b/chipathlon/jobs/scripts/run_music.py
@@ -22,8 +22,8 @@ peak_type_dict = {
     "broad": "-get_multiscale_broad_ERs"
 }
 
-subprocess.call(["/util/opt/lmod/lmod/init/profile"])
-subprocess.call(["module", "load", "music"])
+#subprocess.call(["/util/opt/lmod/lmod/init/profile"])
+#subprocess.call(["module", "load", "music"])
 
 if not os.path.isdir(args.prefix):
     # Create unqiue subdirectories for processing input
@@ -91,8 +91,17 @@ if not os.path.isdir(args.prefix):
             ], stdout=wh, stdin=sort.stdout)
         sort.wait()
 
-        shutil.copyfile("sorted_scale_%s_all.bed" % (scale,),
-            "../%s_sorted_scale_%s_all.bed" % (args.prefix, scale))
+        with open("sorted_scale_%s_all.bed" % (scale,), "r") as rh:
+            with open("../%s_sorted_scale_%s_all.bed" % (args.prefix, scale), "w") as wh:
+                for line in rh:
+                    info = line.split()
+                    # Score value shouldn't be negative
+                    info[4] = -1 * int(info[4])
+                    # pad columsn so there are actually 9
+                    for i in range(0, 3):
+                        info.append(0)
+                    # Write!
+                    wh.write(info.join("\t") + "\n")
 
 else:
     print "Directory %s already exists." % (args.prefix,)
diff --git a/chipathlon/jobs/wrappers/music_wrapper.sh b/chipathlon/jobs/wrappers/music_wrapper.sh
new file mode 100755
index 0000000000000000000000000000000000000000..279e98e31ce7e241b2de3e9ecb11f04a3abee72c
--- /dev/null
+++ b/chipathlon/jobs/wrappers/music_wrapper.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+. /util/opt/lmod/lmod/init/profile
+module load music
+
+run_music.py "$@"
diff --git a/chipathlon/workflow.py b/chipathlon/workflow.py
index de47b7d4188ba303e407dee218e983624e510b49..1f95757a1c11d6f5104309960c91c6f7f25c0c42 100644
--- a/chipathlon/workflow.py
+++ b/chipathlon/workflow.py
@@ -334,7 +334,10 @@ class Workflow(object):
             if "profile" in self.config:
                 for namespace in self.config["profile"]:
                     for key in self.config["profile"][namespace]:
-                        sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, self.config["profile"][namespace][key])
+                        value = self.config["profile"][namespace][key]
+                        if key == "PATH":
+                            value = value + ":%s/jobs/scripts/" % (os.path.dirname(os.path.abspath(__file__)),)
+                        sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, value)
 
             sites += """</site>
                    <site handle="dummylocal" arch="x86_64" os="LINUX">