diff --git a/dx-cwl b/dx-cwl
index c45f3d7..6c3103a 100755
--- a/dx-cwl
+++ b/dx-cwl
@@ -518,7 +518,7 @@ def compile_tool_internal(tool, assets, bundled, folder='/', extradisk=10000, pr
     runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
     runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
     runSpec['distribution'] = "Ubuntu"
-    runSpec['release'] = "14.04"
+    runSpec['release'] = "16.04"
     runSpec['assetDepends'] = []
     runSpec['bundledDepends'] = []
     if assets:
@@ -684,7 +684,7 @@ def compile_scatter_tool(workflow, sname, step, executable_id, folder='/', provi
     runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
     runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
     runSpec['distribution'] = "Ubuntu"
-    runSpec['release'] = "14.04"
+    runSpec['release'] = "16.04"
     runSpec['assetDepends'] = []
     runSpec['bundledDepends'] = []
     if assets:
@@ -861,7 +861,7 @@ def shell_suppress(cmd, ignore_error=False):
     runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
     runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
     runSpec['distribution'] = "Ubuntu"
-    runSpec['release'] = "14.04"
+    runSpec['release'] = "16.04"
     dxapp['runSpec'] = runSpec
     dxapp['access'] = {"project": "CONTRIBUTE", "network": ["*"]}
     with open(dirname+"/dxapp.json", "w") as f:
@@ -918,7 +918,7 @@ def compile_postprocess_tool(workflow, outputs, folder='/', provider='aws'):
     runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
     runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
     runSpec['distribution'] = "Ubuntu"
-    runSpec['release'] = "14.04"
+    runSpec['release'] = "16.04"
     dxapp['runSpec'] = runSpec
     dxapp['access'] = {"project": "CONTRIBUTE", "network": ["*"]}
     with open(dirname+"/dxapp.json", "w") as f:
diff --git a/dx-cwl-applet-code.py b/dx-cwl-applet-code.py
index fc56604..471b31c 100644
--- a/dx-cwl-applet-code.py
+++ b/dx-cwl-applet-code.py
@@ -34,9 +34,6 @@ def shell_suppress(cmd, ignore_error=False):
 def main(**kwargs):
     sh("apt-get update")
     sh("apt-get install python-virtualenv samtools")
-    sh("git clone --recursive https://github.com/dnanexus/dx-toolkit.git")
-    sh("cd dx-toolkit && git checkout 0c818a5cce7164119e7a89d7415770e1ff2caece && cd ..")
-    sh("make -C dx-toolkit python dx-docker")
     os.environ["PATH"] = "/home/dnanexus/dx-toolkit/bin"+":"+os.environ["PATH"]
     os.environ["PYTHONPATH"] = "/home/dnanexus/dx-toolkit/share/dnanexus/lib/python2.7/site-packages:/home/dnanexus/dx-toolkit/lib64/python2.7/site-packages"+":"+os.environ["PYTHONPATH"]
 
@@ -117,7 +114,7 @@ def compile_input_generic(iname, ivalue):
 
     print("Running CWL tool")
     sh("mkdir -p cwloutputs")
-    sh("cwltool --leave-outputs --outdir cwloutputs --user-space-docker-cmd dx-docker tool.cwl cwlinputs.yml > cwl_job_outputs.json")
+    sh("cwltool --leave-outputs --outdir cwloutputs tool.cwl cwlinputs.yml > cwl_job_outputs.json")
 
     print("Process CWL outputs")
     output = {}