diff --git a/deploy/utils/deploy_utils.py b/deploy/utils/deploy_utils.py
index 88b9f1afd..5b0bc477a 100644
--- a/deploy/utils/deploy_utils.py
+++ b/deploy/utils/deploy_utils.py
@@ -4,10 +4,10 @@
 import shutil
 import time
 
-from deploy.utils.shell_utils import run_shell_command
+from utils.shell_utils import run_shell_command
 from deploy.utils.constants import BASE_DIR, DEPLOYMENT_SCRIPTS
-from deploy.utils.other_utils import retrieve_settings, check_kubernetes_context
-from deploy.utils.servctl_utils import render, script_processor, template_processor
+from deploy.utils.servctl_utils import render, script_processor, template_processor, \
+    retrieve_settings, check_kubernetes_context
 
 logger = logging.getLogger()
 
@@ -16,7 +16,7 @@ def deploy(deployment_label, component=None, output_dir=None, other_settings={})
     """
     Args:
         deployment_label (string): one of the DEPLOYMENT_LABELS  (eg. "local", or "gcloud")
-        component (string): optionally specifies one of the components from the DEPLOYABLE_COMPONENTS lists (eg. "postgres" or "phenotips").
+        component (string): optionally specifies one of the components from the DEPLOYABLE_COMPONENTS lists (eg. "elasitsearch").
             If this is set to None, all DEPLOYABLE_COMPONENTS will be deployed in sequence.
         output_dir (string): path of directory where to put deployment logs and rendered config files
         other_settings (dict): a dictionary of other key-value pairs for use during deployment
@@ -49,36 +49,47 @@ def deploy(deployment_label, component=None, output_dir=None, other_settings={})
         logger.info("%s = %s" % (key, value))
 
     # copy settings, templates and scripts to output directory
-    os.chdir("deploy")
-    output_base_dir = os.path.join(output_dir, 'kubernetes/settings')
-    for file_path in glob.glob("kubernetes/templates/*/*.*") + glob.glob("kubernetes/templates/*/*/*.*"):
-        file_path = file_path.replace('kubernetes/templates/', '')
-        input_base_dir = os.path.join(BASE_DIR, 'kubernetes/templates')
+    for file_path in glob.glob("deploy/kubernetes/templates/*/*.*") + glob.glob("deploy/kubernetes/templates/*/*/*.*"):
+        file_path = file_path.replace('deploy/kubernetes/templates/', '')
+        input_base_dir = os.path.join(BASE_DIR, 'deploy/kubernetes/templates')
+        output_base_dir = os.path.join(output_dir, 'deploy/kubernetes/configs')
         render(template_processor, input_base_dir, file_path, settings, output_base_dir)
 
-    for file_path in glob.glob(os.path.join("kubernetes/scripts/*.sh")):
+    for file_path in glob.glob(os.path.join("deploy/kubernetes/scripts/*.sh")):
         render(script_processor, BASE_DIR, file_path, settings, output_dir)
 
-    for file_path in glob.glob(os.path.join("kubernetes/scripts/*.py")):
-        shutil.copy(file_path, output_base_dir)
+    #for file_path in glob.glob(os.path.join("kubernetes/scripts/*.py")):
+    #    shutil.copy(file_path, output_base_dir)
 
-    for file_path in glob.glob(os.path.join("settings/*.yaml")):
-        shutil.copy(file_path, output_base_dir)
+    for file_path in glob.glob(os.path.join("deploy/kubernetes/settings/*.yaml")):
+        try:
+            os.makedirs(os.path.join(output_dir, os.path.dirname(file_path)))
+        except OSError as e:
+            # ignore if the error is that the directory already exists
+            # TODO after switch to python3, use exist_ok arg
+            if "File exists" not in str(e):
+                raise
+
+        shutil.copy(file_path, os.path.join(output_dir, file_path))
 
     # copy docker directory to output directory
-    docker_src_dir = os.path.join(BASE_DIR, "docker/")
-    docker_dest_dir = os.path.join(output_dir, "docker")
+    docker_src_dir = os.path.join(BASE_DIR, "deploy/docker/")
+    docker_dest_dir = os.path.join(output_dir, "deploy/docker")
     logger.info("Copying %(docker_src_dir)s to %(docker_dest_dir)s" % locals())
     shutil.copytree(docker_src_dir, docker_dest_dir)
 
+    # write out ConfigMap file so that settings key/values can be added as environment variables in each of the pods
+    with open(os.path.join(output_dir, "deploy/kubernetes/settings/all-settings.properties"), "w") as f:
+        for key, value in settings.items():
+            f.write("%s=%s\n" % (key, value))
 
     # deploy
     if component:
         deployment_scripts = [s for s in DEPLOYMENT_SCRIPTS if 'deploy_begin' in s or component in s or component.replace('-', '_') in s]
     else:
-        deployment_scripts = [s for s in DEPLOYMENT_SCRIPTS] # don't deploy these by default
+        deployment_scripts = DEPLOYMENT_SCRIPTS
 
-    os.chdir(output_dir)
+    os.chdir(os.path.join(output_dir, "deploy"))
     logger.info("Switched to %(output_dir)s" % locals())
 
     for path in deployment_scripts: