diff --git a/bin/mapDamage b/bin/mapDamage
index 7e3fa86..d64eb4e 100755
--- a/bin/mapDamage
+++ b/bin/mapDamage
@@ -163,14 +163,6 @@ def main():
         sys.path.insert(0,path_to_mm)
     import mapdamage
 
-    fpath_seqtk = mapdamage.rscript.construct_path("seqtk", folder="seqtk")
-    if not (os.path.isfile(fpath_seqtk) and os.access(fpath_seqtk, os.X_OK)):
-        sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"
-                         "been intalled properly or current user does not\n"
-                         "sufficient permissions. Expected executable at\n   "
-                         "'%s'\n" % (fpath_seqtk,))
-        return 1
-
     options = mapdamage.parseoptions.options()
     if options == None:
         sys.stderr.write("Option parsing failed, terminating the program\n")
diff --git a/mapdamage/composition.py b/mapdamage/composition.py
index b46b9d6..99edbed 100644
--- a/mapdamage/composition.py
+++ b/mapdamage/composition.py
@@ -33,11 +33,10 @@ def get_base_comp(filename,destination=False):
     Gets the basecomposition of all the sequences in filename
     and returns the value to destination if given.
     """
-    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk")
     bases = {"A":0,"C":0,"G":0,"T":0}
     alp = ["A","C","G","T"]
     try:
-        proc = subprocess.Popen([path_to_seqtk,"comp",filename],stdout=subprocess.PIPE)
+        proc = subprocess.Popen(["seqtk","comp",filename],stdout=subprocess.PIPE)
         out = proc.communicate()[0]
         for li in out.splitlines():
             tabs = li.split() # 1 is the ref, 2 is the total and then the base counts A, C, G and T.
diff --git a/setup.py b/setup.py
index 6e93d8e..c1ad8c7 100644
--- a/setup.py
+++ b/setup.py
@@ -45,13 +45,7 @@ class compileInstall(DistutilsInstall):
     def run(self):
         self.record=""
         setup_version()
-        compile_seqtk()
         DistutilsInstall.run(self)
-        # fixing the permission problem of seqtk
-        files = self.get_outputs()
-        for fi in files:
-            if fi.endswith("seqtk/seqtk"):
-                os.chmod(fi,0o755)