diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 46a7e3d..12d2f01 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -29,7 +29,7 @@
     },
     "features": {
         // add in eternal history and other bash features
-        "ghcr.io/diamondlightsource/devcontainer-features/bash-config:1.0.0": {}
+        "ghcr.io/diamondlightsource/devcontainer-features/bash-config:1": {}
     },
     // Create the config folder for the bash-config feature
     "initializeCommand": "mkdir -p ${localEnv:HOME}/.config/bash-config",
@@ -42,7 +42,11 @@
         "--device=/dev/fuse"
     ],
     "mounts": [
-        "source=/dls_sw/,target=/dls_sw,type=bind,consistency=cached"
+        "source=/dls_sw/,target=/dls_sw,type=bind,consistency=cached",
+        // these two mounts allow us to pick up cache and config folders that have
+        // been symlinked out of the home directory
+        "source=/dls/science/users/,target=/dls/science/users,type=bind,consistency=cached",
+        "source=/scratch/,target=/scratch,type=bind,consistency=cached"
     ],
     // Mount the parent as /workspaces so we can pip install peers as editable
     "workspaceMount": "source=${localWorkspaceFolder}/..,target=/workspaces,type=bind",
diff --git a/.github/workflows/_test.yml b/.github/workflows/_test.yml
index f652d41..b8e4ba6 100644
--- a/.github/workflows/_test.yml
+++ b/.github/workflows/_test.yml
@@ -51,7 +51,13 @@ jobs:
           pip-install: ".[dev]"
 
       - name: Run tests
-        run: tox -e tests
+        run: |
+          sudo apt update
+          sudo apt install -y software-properties-common
+          sudo add-apt-repository -y ppa:apptainer/ppa
+          sudo apt update
+          sudo apt install -y apptainer
+          tox -e tests
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index 5eda15c..c602ca4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -72,3 +72,6 @@ lockfiles/
 
 # Demo output path for vscode tasks
 demo-output
+
+# vscode workspaces are local only
+*.code-workspace
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
index da89333..f60d802 100644
--- a/.vscode/tasks.json
+++ b/.vscode/tasks.json
@@ -42,6 +42,15 @@
             "command": "deploy-tools compare ${input:compare-mode} ${input:deploy-folder}",
             "problemMatcher": []
         },
+        {
+            "type": "shell",
+            "label": "Recreate tests sample output from demo_configuration",
+            "command": "tests/generate_samples.sh",
+            "options": {
+                "cwd": "${workspaceRoot}"
+            },
+            "problemMatcher": [],
+        },
     ],
     "inputs": [
         {
diff --git a/src/deploy_tools/app_builder.py b/src/deploy_tools/app_builder.py
index 7e4dc41..f4b019a 100644
--- a/src/deploy_tools/app_builder.py
+++ b/src/deploy_tools/app_builder.py
@@ -44,6 +44,9 @@ def _create_apptainer_files(self, app: ApptainerApp, module: Module) -> None:
             entrypoint_file = entrypoints_folder / entrypoint.name
 
             mounts = ",".join(chain(global_options.mounts, options.mounts)).strip()
+            host_binaries = " ".join(
+                chain(global_options.host_binaries, options.host_binaries)
+            ).strip()
 
             apptainer_args = f"{global_options.apptainer_args} {options.apptainer_args}"
             apptainer_args = apptainer_args.strip()
@@ -55,6 +58,7 @@ def _create_apptainer_files(self, app: ApptainerApp, module: Module) -> None:
 
             params = {
                 "mounts": mounts,
+                "host_binaries": host_binaries,
                 "apptainer_args": apptainer_args,
                 "relative_sif_file": relative_sif_file,
                 "command": command,
diff --git a/src/deploy_tools/demo_configuration/edge-containers-cli/0.1.yaml b/src/deploy_tools/demo_configuration/edge-containers-cli/0.1.yaml
new file mode 100644
index 0000000..8dc38bb
--- /dev/null
+++ b/src/deploy_tools/demo_configuration/edge-containers-cli/0.1.yaml
@@ -0,0 +1,54 @@
+# yaml-language-server: $schema=/workspaces/deploy-tools/src/deploy_tools/models/schemas/release.json
+
+module:
+  name: edge-containers-cli
+  version: "0.1"
+  description: ec command line tool for kubernetes IOCs
+
+  env_vars:
+    # For host-binaries PR we will use the K8S backend - this will be changed to
+    # ARGOCD when we add in the BinaryApp feature (upcoming PR)
+    - name: EC_CLI_BACKEND
+      value: K8S
+    - name: EC_LOG_URL
+      value: "https://graylog.diamond.ac.uk/search?rangetype=relative&fields=message%2Csource&width=1489&highlightMessage=&relative=172800&q=pod_name%3A{service_name}*"
+    # The default configuration is for p47 for testing
+    - name: EC_TARGET
+      value: p47-beamline # K8S target
+      # value: p47-beamline/p47 # Argocd target
+    - name: EC_SERVICES_REPO
+      value: https://github.com/epics-containers/p47-services
+
+  applications:
+    - app_type: apptainer
+
+      container:
+        path: docker://ghcr.io/epics-containers/edge-containers-cli
+        version: "4.4.1"
+
+      entrypoints:
+        - name: ec
+          command: ec
+        # for debugging enter the container with bash shell
+        - name: ec-bash
+          command: bash
+
+      global_options:
+        mounts:
+          # places to get argocd and kubectl config from
+          - /dls/science/users/:/dls/science/users/
+          - /scratch:/scratch
+          - /dls_sw/apps:/dls_sw/apps
+        host_binaries:
+          - kubectl
+          - helm
+          - kubelogin
+          - klogout
+          - kustomize
+          - kubeseal
+          - kubectl-oidc_login
+
+    - app_type: shell
+      name: ec-login
+      script:
+        - argocd login argocd.diamond.ac.uk --grpc-web --sso
diff --git a/src/deploy_tools/models/apptainer_app.py b/src/deploy_tools/models/apptainer_app.py
index 35c6bf2..dda8411 100644
--- a/src/deploy_tools/models/apptainer_app.py
+++ b/src/deploy_tools/models/apptainer_app.py
@@ -1,13 +1,37 @@
 from collections.abc import Sequence
-from typing import Literal
+from typing import Annotated, Literal
+
+from pydantic import Field
 
 from .parent import ParentModel
 
 
 class EntrypointOptions(ParentModel):
-    apptainer_args: str = ""
-    command_args: str = ""
-    mounts: Sequence[str] = []
+    apptainer_args: Annotated[
+        str,
+        Field(description="Apptainer arguments to pass when launching the container"),
+    ] = ""
+
+    command_args: Annotated[
+        str, Field(description="Arguments to pass to command entrypoint")
+    ] = ""
+
+    mounts: Annotated[
+        Sequence[str],
+        Field(
+            description="A list of mount points to add to the container in the form of "
+            "'host_path:container_path'"
+        ),
+    ] = []
+
+    host_binaries: Annotated[
+        Sequence[str],
+        Field(
+            description="A list of host binaries to mount into the container. "
+            "These are discovered on the host using the current PATH and are "
+            "mounted into the container at /usr/bin/<binary_name>."
+        ),
+    ] = []
 
 
 class Entrypoint(ParentModel):
diff --git a/src/deploy_tools/models/schemas/deployment.json b/src/deploy_tools/models/schemas/deployment.json
index 3ee93bc..1746d19 100644
--- a/src/deploy_tools/models/schemas/deployment.json
+++ b/src/deploy_tools/models/schemas/deployment.json
@@ -1,6 +1,6 @@
 {
   "$defs": {
-    "Apptainer": {
+    "ApptainerApp": {
       "additionalProperties": false,
       "description": "Represents an Apptainer application or set of applications for a single image.\n\nThis uses Apptainer to deploy a portable image of the desired container. Several\nentrypoints can then be specified to allow for multiple commands run on the same\ncontainer image.",
       "properties": {
@@ -24,7 +24,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -33,7 +34,7 @@
         "container",
         "entrypoints"
       ],
-      "title": "Apptainer",
+      "title": "ApptainerApp",
       "type": "object"
     },
     "ContainerImage": {
@@ -98,7 +99,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -113,21 +115,33 @@
       "properties": {
         "apptainer_args": {
           "default": "",
+          "description": "Apptainer arguments to pass when launching the container",
           "title": "Apptainer Args",
           "type": "string"
         },
         "command_args": {
           "default": "",
+          "description": "Arguments to pass to command entrypoint",
           "title": "Command Args",
           "type": "string"
         },
         "mounts": {
           "default": [],
+          "description": "A list of mount points to add to the container in the form of 'host_path:container_path'",
           "items": {
             "type": "string"
           },
           "title": "Mounts",
           "type": "array"
+        },
+        "host_binaries": {
+          "default": [],
+          "description": "A list of host binaries to mount into the container. These are discovered on the host using the current PATH and are mounted into the container at /usr/bin/<binary_name>.",
+          "items": {
+            "type": "string"
+          },
+          "title": "Host Binaries",
+          "type": "array"
         }
       },
       "title": "EntrypointOptions",
@@ -197,17 +211,17 @@
           "items": {
             "discriminator": {
               "mapping": {
-                "apptainer": "#/$defs/Apptainer",
-                "shell": "#/$defs/Shell"
+                "apptainer": "#/$defs/ApptainerApp",
+                "shell": "#/$defs/ShellApp"
               },
               "propertyName": "app_type"
             },
             "oneOf": [
               {
-                "$ref": "#/$defs/Apptainer"
+                "$ref": "#/$defs/ApptainerApp"
               },
               {
-                "$ref": "#/$defs/Shell"
+                "$ref": "#/$defs/ShellApp"
               }
             ]
           },
@@ -281,7 +295,7 @@
       },
       "type": "object"
     },
-    "Shell": {
+    "ShellApp": {
       "additionalProperties": false,
       "description": "Represents a Shell application.\n\nThis will run the code specified as a shell script. This currently uses Bash for\nimproved functionality while retaining high compatibility with various Linux\ndistributions.",
       "properties": {
@@ -307,7 +321,7 @@
         "name",
         "script"
       ],
-      "title": "Shell",
+      "title": "ShellApp",
       "type": "object"
     }
   },
diff --git a/src/deploy_tools/models/schemas/module.json b/src/deploy_tools/models/schemas/module.json
index e7a877e..8007d8b 100644
--- a/src/deploy_tools/models/schemas/module.json
+++ b/src/deploy_tools/models/schemas/module.json
@@ -1,6 +1,6 @@
 {
   "$defs": {
-    "Apptainer": {
+    "ApptainerApp": {
       "additionalProperties": false,
       "description": "Represents an Apptainer application or set of applications for a single image.\n\nThis uses Apptainer to deploy a portable image of the desired container. Several\nentrypoints can then be specified to allow for multiple commands run on the same\ncontainer image.",
       "properties": {
@@ -24,7 +24,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -33,7 +34,7 @@
         "container",
         "entrypoints"
       ],
-      "title": "Apptainer",
+      "title": "ApptainerApp",
       "type": "object"
     },
     "ContainerImage": {
@@ -80,7 +81,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -95,21 +97,33 @@
       "properties": {
         "apptainer_args": {
           "default": "",
+          "description": "Apptainer arguments to pass when launching the container",
           "title": "Apptainer Args",
           "type": "string"
         },
         "command_args": {
           "default": "",
+          "description": "Arguments to pass to command entrypoint",
           "title": "Command Args",
           "type": "string"
         },
         "mounts": {
           "default": [],
+          "description": "A list of mount points to add to the container in the form of 'host_path:container_path'",
           "items": {
             "type": "string"
           },
           "title": "Mounts",
           "type": "array"
+        },
+        "host_binaries": {
+          "default": [],
+          "description": "A list of host binaries to mount into the container. These are discovered on the host using the current PATH and are mounted into the container at /usr/bin/<binary_name>.",
+          "items": {
+            "type": "string"
+          },
+          "title": "Host Binaries",
+          "type": "array"
         }
       },
       "title": "EntrypointOptions",
@@ -179,17 +193,17 @@
           "items": {
             "discriminator": {
               "mapping": {
-                "apptainer": "#/$defs/Apptainer",
-                "shell": "#/$defs/Shell"
+                "apptainer": "#/$defs/ApptainerApp",
+                "shell": "#/$defs/ShellApp"
               },
               "propertyName": "app_type"
             },
             "oneOf": [
               {
-                "$ref": "#/$defs/Apptainer"
+                "$ref": "#/$defs/ApptainerApp"
               },
               {
-                "$ref": "#/$defs/Shell"
+                "$ref": "#/$defs/ShellApp"
               }
             ]
           },
@@ -232,7 +246,7 @@
       "title": "ModuleDependency",
       "type": "object"
     },
-    "Shell": {
+    "ShellApp": {
       "additionalProperties": false,
       "description": "Represents a Shell application.\n\nThis will run the code specified as a shell script. This currently uses Bash for\nimproved functionality while retaining high compatibility with various Linux\ndistributions.",
       "properties": {
@@ -258,7 +272,7 @@
         "name",
         "script"
       ],
-      "title": "Shell",
+      "title": "ShellApp",
       "type": "object"
     }
   },
diff --git a/src/deploy_tools/models/schemas/release.json b/src/deploy_tools/models/schemas/release.json
index e7a877e..8007d8b 100644
--- a/src/deploy_tools/models/schemas/release.json
+++ b/src/deploy_tools/models/schemas/release.json
@@ -1,6 +1,6 @@
 {
   "$defs": {
-    "Apptainer": {
+    "ApptainerApp": {
       "additionalProperties": false,
       "description": "Represents an Apptainer application or set of applications for a single image.\n\nThis uses Apptainer to deploy a portable image of the desired container. Several\nentrypoints can then be specified to allow for multiple commands run on the same\ncontainer image.",
       "properties": {
@@ -24,7 +24,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -33,7 +34,7 @@
         "container",
         "entrypoints"
       ],
-      "title": "Apptainer",
+      "title": "ApptainerApp",
       "type": "object"
     },
     "ContainerImage": {
@@ -80,7 +81,8 @@
           "default": {
             "apptainer_args": "",
             "command_args": "",
-            "mounts": []
+            "mounts": [],
+            "host_binaries": []
           }
         }
       },
@@ -95,21 +97,33 @@
       "properties": {
         "apptainer_args": {
           "default": "",
+          "description": "Apptainer arguments to pass when launching the container",
           "title": "Apptainer Args",
           "type": "string"
         },
         "command_args": {
           "default": "",
+          "description": "Arguments to pass to command entrypoint",
           "title": "Command Args",
           "type": "string"
         },
         "mounts": {
           "default": [],
+          "description": "A list of mount points to add to the container in the form of 'host_path:container_path'",
           "items": {
             "type": "string"
           },
           "title": "Mounts",
           "type": "array"
+        },
+        "host_binaries": {
+          "default": [],
+          "description": "A list of host binaries to mount into the container. These are discovered on the host using the current PATH and are mounted into the container at /usr/bin/<binary_name>.",
+          "items": {
+            "type": "string"
+          },
+          "title": "Host Binaries",
+          "type": "array"
         }
       },
       "title": "EntrypointOptions",
@@ -179,17 +193,17 @@
           "items": {
             "discriminator": {
               "mapping": {
-                "apptainer": "#/$defs/Apptainer",
-                "shell": "#/$defs/Shell"
+                "apptainer": "#/$defs/ApptainerApp",
+                "shell": "#/$defs/ShellApp"
               },
               "propertyName": "app_type"
             },
             "oneOf": [
               {
-                "$ref": "#/$defs/Apptainer"
+                "$ref": "#/$defs/ApptainerApp"
               },
               {
-                "$ref": "#/$defs/Shell"
+                "$ref": "#/$defs/ShellApp"
               }
             ]
           },
@@ -232,7 +246,7 @@
       "title": "ModuleDependency",
       "type": "object"
     },
-    "Shell": {
+    "ShellApp": {
       "additionalProperties": false,
       "description": "Represents a Shell application.\n\nThis will run the code specified as a shell script. This currently uses Bash for\nimproved functionality while retaining high compatibility with various Linux\ndistributions.",
       "properties": {
@@ -258,7 +272,7 @@
         "name",
         "script"
       ],
-      "title": "Shell",
+      "title": "ShellApp",
       "type": "object"
     }
   },
diff --git a/src/deploy_tools/templater.py b/src/deploy_tools/templater.py
index 11d44f4..3c77daa 100644
--- a/src/deploy_tools/templater.py
+++ b/src/deploy_tools/templater.py
@@ -50,7 +50,10 @@ def create(
 
         open_mode = "w" if overwrite else "x"
         with open(output_file, open_mode) as f:
-            f.write(self._templates[template].render(**parameters))
+            rendered = self._templates[template].render(**parameters)
+            # enforce single trailing newline for pre-commit goodness
+            rendered = rendered.strip() + "\n"
+            f.write(rendered)
 
         permissions = EXECUTABLE_PERMISSIONS if executable else DEFAULT_PERMISSIONS
         output_file.chmod(permissions)
diff --git a/src/deploy_tools/templates/apptainer_entrypoint b/src/deploy_tools/templates/apptainer_entrypoint
index da9a834..bb9d350 100644
--- a/src/deploy_tools/templates/apptainer_entrypoint
+++ b/src/deploy_tools/templates/apptainer_entrypoint
@@ -23,6 +23,12 @@ if [[ ! -f ${sif_file} ]]; then
     exit 1
 fi
 
+# add mounts of host binaries into /usr/bin
+for i in {{ host_binaries }}; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
 # Set up mounts if any have been configured
 if [[ ! -z ${mounts} ]]; then
     opts="-B ${mounts}"
@@ -31,5 +37,8 @@ fi
 opts=${opts}" --env DISPLAY=${DISPLAY}"
 opts=${opts}" ${apptainer_args}"
 
-set -x
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
 apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/src/deploy_tools/templates/shell_entrypoint b/src/deploy_tools/templates/shell_entrypoint
index 5c83fa2..8bc7087 100644
--- a/src/deploy_tools/templates/shell_entrypoint
+++ b/src/deploy_tools/templates/shell_entrypoint
@@ -1,5 +1,9 @@
 #! /bin/bash
 
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
 {% for line in script -%}
 {{ line }}
 {% endfor %}
diff --git a/tests/conftest.py b/tests/conftest.py
index ebe9c10..9a58980 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,21 @@
 import os
+from pathlib import Path
 from typing import Any
 
 import pytest
+from typer.testing import CliRunner
+
+from deploy_tools.__main__ import app
+
+runner = CliRunner()
+
+
+def run_cli(*args):
+    result = runner.invoke(app, [str(x) for x in args])
+    if result.exception:
+        raise result.exception
+    assert result.exit_code == 0, result
+
 
 # Prevent pytest from catching exceptions when debugging in vscode so that break on
 # exception works correctly (see: https://github.com/pytest-dev/pytest/issues/7409)
@@ -19,3 +33,18 @@ def pytest_exception_interact(call: pytest.CallInfo[Any]):
     @pytest.hookimpl(tryfirst=True)
     def pytest_internalerror(excinfo: pytest.ExceptionInfo[Any]):
         raise excinfo.value
+
+
+@pytest.fixture
+def samples():
+    return Path(__file__).parent / "samples"
+
+
+@pytest.fixture
+def schemas():
+    return Path(__file__).parent.parent / "src" / "deploy_tools" / "models" / "schemas"
+
+
+@pytest.fixture
+def demo_config():
+    return Path(__file__).parent.parent / "src" / "deploy_tools" / "demo_configuration"
diff --git a/tests/generate_samples.sh b/tests/generate_samples.sh
new file mode 100755
index 0000000..736c713
--- /dev/null
+++ b/tests/generate_samples.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+set -xe
+
+THIS_DIR=$(realpath $(dirname ${0}))
+SAMPLES_DIR=${THIS_DIR}/samples
+TMP_DIR=/tmp/deploy-tools-output
+
+rm -rf "${SAMPLES_DIR}"
+rm -rf "${TMP_DIR}"
+mkdir -p "${TMP_DIR}"
+
+deploy-tools sync --from-scratch ${TMP_DIR} ${THIS_DIR}/../src/deploy_tools/demo_configuration
+
+# don't keep the sif or git files!
+rm -rf $(find ${TMP_DIR} -name "*.sif")
+rm -rf ${TMP_DIR}/.git*
+
+rm -rf ${SAMPLES_DIR}
+mkdir -p ${SAMPLES_DIR}
+cp -r ${TMP_DIR} ${SAMPLES_DIR}
+<<<<<<< HEAD
+=======
+
+>>>>>>> ce3367b (add test for demo_configuration)
diff --git a/tests/samples/deploy-tools-output/deployment.yaml b/tests/samples/deploy-tools-output/deployment.yaml
new file mode 100644
index 0000000..ced3c36
--- /dev/null
+++ b/tests/samples/deploy-tools-output/deployment.yaml
@@ -0,0 +1,213 @@
+releases:
+  dls-pmac-control:
+    '0.1':
+      deprecated: false
+      module:
+        applications:
+        - app_type: apptainer
+          container:
+            path: docker://ghcr.io/diamondlightsource/dls-pmac-control
+            version: 3.2.0b1
+          entrypoints:
+          - command: dls-pmac-control
+            name: dls-pmac-control
+            options:
+              apptainer_args: -e
+              command_args: ''
+              host_binaries: []
+              mounts: []
+          global_options:
+            apptainer_args: ''
+            command_args: ''
+            host_binaries: []
+            mounts: []
+        - app_type: shell
+          name: test-echo-module-file
+          script:
+          - echo $EXAMPLE_VALUE
+        dependencies: []
+        description: Demonstration of the deploy-tools process
+        env_vars:
+        - name: EXAMPLE_VALUE
+          value: Test message EXAMPLE_VALUE from example-module-file version 0.1
+        name: dls-pmac-control
+        version: '0.1'
+    '0.2':
+      deprecated: false
+      module:
+        applications:
+        - app_type: apptainer
+          container:
+            path: docker://ghcr.io/diamondlightsource/dls-pmac-control
+            version: 3.2.0b1
+          entrypoints:
+          - command: dls-pmac-control
+            name: dls-pmac-control
+            options:
+              apptainer_args: -e
+              command_args: ''
+              host_binaries: []
+              mounts: []
+          global_options:
+            apptainer_args: ''
+            command_args: ''
+            host_binaries: []
+            mounts: []
+        - app_type: shell
+          name: test-echo-module-file
+          script:
+          - echo $EXAMPLE_VALUE
+        dependencies: []
+        description: Demonstration of the deploy-tools process
+        env_vars:
+        - name: EXAMPLE_VALUE
+          value: Test message EXAMPLE_VALUE from example-module-file version 0.2
+        name: dls-pmac-control
+        version: '0.2'
+  edge-containers-cli:
+    '0.1':
+      deprecated: false
+      module:
+        applications:
+        - app_type: apptainer
+          container:
+            path: docker://ghcr.io/epics-containers/edge-containers-cli
+            version: 4.4.1
+          entrypoints:
+          - command: ec
+            name: ec
+            options:
+              apptainer_args: ''
+              command_args: ''
+              host_binaries: []
+              mounts: []
+          - command: bash
+            name: ec-bash
+            options:
+              apptainer_args: ''
+              command_args: ''
+              host_binaries: []
+              mounts: []
+          global_options:
+            apptainer_args: ''
+            command_args: ''
+            host_binaries:
+            - kubectl
+            - helm
+            - kubelogin
+            - klogout
+            - kustomize
+            - kubeseal
+            - kubectl-oidc_login
+            mounts:
+            - /dls/science/users/:/dls/science/users/
+            - /scratch:/scratch
+            - /dls_sw/apps:/dls_sw/apps
+        - app_type: shell
+          name: ec-login
+          script:
+          - argocd login argocd.diamond.ac.uk --grpc-web --sso
+        dependencies: []
+        description: ec command line tool for kubernetes IOCs
+        env_vars:
+        - name: EC_CLI_BACKEND
+          value: K8S
+        - name: EC_LOG_URL
+          value: https://graylog.diamond.ac.uk/search?rangetype=relative&fields=message%2Csource&width=1489&highlightMessage=&relative=172800&q=pod_name%3A{service_name}*
+        - name: EC_TARGET
+          value: p47-beamline
+        - name: EC_SERVICES_REPO
+          value: https://github.com/epics-containers/p47-services
+        name: edge-containers-cli
+        version: '0.1'
+  example-module-apps:
+    '0.1':
+      deprecated: false
+      module:
+        applications:
+        - app_type: apptainer
+          container:
+            path: docker://ghcr.io/apptainer/lolcow
+            version: latest
+          entrypoints:
+          - command: cowsay
+            name: cowsay-hello
+            options:
+              apptainer_args: ''
+              command_args: Hello
+              host_binaries: []
+              mounts: []
+          - command: ls
+            name: show-directory
+            options:
+              apptainer_args: ''
+              command_args: -al /dls_sw_test
+              host_binaries: []
+              mounts: []
+          global_options:
+            apptainer_args: ''
+            command_args: ''
+            host_binaries: []
+            mounts:
+            - /dls_sw:/dls_sw_test:ro
+        - app_type: shell
+          name: test-echo-module-folder
+          script:
+          - echo $OTHER_VALUE
+        - app_type: shell
+          name: test-shell-script
+          script:
+          - echo This is the first line of a shell script
+          - echo and this is the second line.
+          - echo Your input is ${1}
+        dependencies: []
+        description: Demonstration of a module configuration folder
+        env_vars:
+        - name: OTHER_VALUE
+          value: Test message OTHER_VALUE from example-module-folder
+        name: example-module-apps
+        version: '0.1'
+  example-module-deps:
+    '0.2':
+      deprecated: false
+      module:
+        applications: []
+        dependencies:
+        - name: dls-pmac-control
+          version: '0.1'
+        - name: example-module-apps
+          version: '0.1'
+        description: Demonstration of deploy-tools dependencies
+        env_vars: []
+        name: example-module-deps
+        version: '0.2'
+  phoebus:
+    '0.1':
+      deprecated: false
+      module:
+        applications:
+        - app_type: apptainer
+          container:
+            path: docker://ghcr.io/epics-containers/ec-phoebus
+            version: 4.7.3ec2
+          entrypoints:
+          - command: java -jar /phoebus/phoebus.jar -server 7010
+            name: phoebus
+            options:
+              apptainer_args: --env DISPLAY=${DISPLAY} -e
+              command_args: -server 7010
+              host_binaries: []
+              mounts: []
+          global_options:
+            apptainer_args: ''
+            command_args: ''
+            host_binaries: []
+            mounts: []
+        dependencies: []
+        description: Containerised release of CSS Phoebus
+        env_vars: []
+        name: phoebus
+        version: '0.1'
+settings:
+  default_versions:
+    dls-pmac-control: '0.1'
diff --git a/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/.version b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/.version
new file mode 100644
index 0000000..d9b8f92
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/.version
@@ -0,0 +1,2 @@
+#%Module1.0
+set ModulesVersion 0.1
diff --git a/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.1 b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.1
new file mode 120000
index 0000000..75b7024
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.1
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/dls-pmac-control/0.1/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.2 b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.2
new file mode 120000
index 0000000..0c56729
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/dls-pmac-control/0.2
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/dls-pmac-control/0.2/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/.version b/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/.version
new file mode 100644
index 0000000..d9b8f92
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/.version
@@ -0,0 +1,2 @@
+#%Module1.0
+set ModulesVersion 0.1
diff --git a/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/0.1 b/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/0.1
new file mode 120000
index 0000000..00b90c0
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/edge-containers-cli/0.1
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/edge-containers-cli/0.1/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modulefiles/example-module-apps/.version b/tests/samples/deploy-tools-output/modulefiles/example-module-apps/.version
new file mode 100644
index 0000000..d9b8f92
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/example-module-apps/.version
@@ -0,0 +1,2 @@
+#%Module1.0
+set ModulesVersion 0.1
diff --git a/tests/samples/deploy-tools-output/modulefiles/example-module-apps/0.1 b/tests/samples/deploy-tools-output/modulefiles/example-module-apps/0.1
new file mode 120000
index 0000000..53b9057
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/example-module-apps/0.1
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/example-module-apps/0.1/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modulefiles/example-module-deps/.version b/tests/samples/deploy-tools-output/modulefiles/example-module-deps/.version
new file mode 100644
index 0000000..26a66b4
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/example-module-deps/.version
@@ -0,0 +1,2 @@
+#%Module1.0
+set ModulesVersion 0.2
diff --git a/tests/samples/deploy-tools-output/modulefiles/example-module-deps/0.2 b/tests/samples/deploy-tools-output/modulefiles/example-module-deps/0.2
new file mode 120000
index 0000000..cd04ecd
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/example-module-deps/0.2
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/example-module-deps/0.2/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modulefiles/phoebus/.version b/tests/samples/deploy-tools-output/modulefiles/phoebus/.version
new file mode 100644
index 0000000..d9b8f92
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/phoebus/.version
@@ -0,0 +1,2 @@
+#%Module1.0
+set ModulesVersion 0.1
diff --git a/tests/samples/deploy-tools-output/modulefiles/phoebus/0.1 b/tests/samples/deploy-tools-output/modulefiles/phoebus/0.1
new file mode 120000
index 0000000..5468b29
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modulefiles/phoebus/0.1
@@ -0,0 +1 @@
+/tmp/deploy-tools-output/modules/phoebus/0.1/modulefile
\ No newline at end of file
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/dls-pmac-control b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/dls-pmac-control
new file mode 100755
index 0000000..e09f6b4
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/dls-pmac-control
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts=""
+# Additional arguments for apptainer
+apptainer_args="-e"
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/a2c305dc6e8732efbb76b32c89f884f4.sif"
+# Command to run in container
+command="dls-pmac-control"
+# Options and arguments to pass to command
+command_args=""
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in ; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/test-echo-module-file b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/test-echo-module-file
new file mode 100755
index 0000000..6da99f6
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints/test-echo-module-file
@@ -0,0 +1,7 @@
+#! /bin/bash
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
+echo $EXAMPLE_VALUE
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/module.yaml b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/module.yaml
new file mode 100644
index 0000000..6ba35a7
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/module.yaml
@@ -0,0 +1,29 @@
+applications:
+- app_type: apptainer
+  container:
+    path: docker://ghcr.io/diamondlightsource/dls-pmac-control
+    version: 3.2.0b1
+  entrypoints:
+  - command: dls-pmac-control
+    name: dls-pmac-control
+    options:
+      apptainer_args: -e
+      command_args: ''
+      host_binaries: []
+      mounts: []
+  global_options:
+    apptainer_args: ''
+    command_args: ''
+    host_binaries: []
+    mounts: []
+- app_type: shell
+  name: test-echo-module-file
+  script:
+  - echo $EXAMPLE_VALUE
+dependencies: []
+description: Demonstration of the deploy-tools process
+env_vars:
+- name: EXAMPLE_VALUE
+  value: Test message EXAMPLE_VALUE from example-module-file version 0.1
+name: dls-pmac-control
+version: '0.1'
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/modulefile b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/modulefile
new file mode 100644
index 0000000..2f27e87
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.1/modulefile
@@ -0,0 +1,10 @@
+#%Module1.0
+##
+## dls-pmac-control - Demonstration of the deploy-tools process
+##
+module-whatis "Demonstration of the deploy-tools process"
+
+setenv EXAMPLE_VALUE "Test message EXAMPLE_VALUE from example-module-file version 0.1"
+
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/dls-pmac-control/0.1/entrypoints"
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/dls-pmac-control b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/dls-pmac-control
new file mode 100755
index 0000000..e09f6b4
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/dls-pmac-control
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts=""
+# Additional arguments for apptainer
+apptainer_args="-e"
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/a2c305dc6e8732efbb76b32c89f884f4.sif"
+# Command to run in container
+command="dls-pmac-control"
+# Options and arguments to pass to command
+command_args=""
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in ; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/test-echo-module-file b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/test-echo-module-file
new file mode 100755
index 0000000..6da99f6
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints/test-echo-module-file
@@ -0,0 +1,7 @@
+#! /bin/bash
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
+echo $EXAMPLE_VALUE
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/module.yaml b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/module.yaml
new file mode 100644
index 0000000..3b0c95b
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/module.yaml
@@ -0,0 +1,29 @@
+applications:
+- app_type: apptainer
+  container:
+    path: docker://ghcr.io/diamondlightsource/dls-pmac-control
+    version: 3.2.0b1
+  entrypoints:
+  - command: dls-pmac-control
+    name: dls-pmac-control
+    options:
+      apptainer_args: -e
+      command_args: ''
+      host_binaries: []
+      mounts: []
+  global_options:
+    apptainer_args: ''
+    command_args: ''
+    host_binaries: []
+    mounts: []
+- app_type: shell
+  name: test-echo-module-file
+  script:
+  - echo $EXAMPLE_VALUE
+dependencies: []
+description: Demonstration of the deploy-tools process
+env_vars:
+- name: EXAMPLE_VALUE
+  value: Test message EXAMPLE_VALUE from example-module-file version 0.2
+name: dls-pmac-control
+version: '0.2'
diff --git a/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/modulefile b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/modulefile
new file mode 100644
index 0000000..f524b6a
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/dls-pmac-control/0.2/modulefile
@@ -0,0 +1,10 @@
+#%Module1.0
+##
+## dls-pmac-control - Demonstration of the deploy-tools process
+##
+module-whatis "Demonstration of the deploy-tools process"
+
+setenv EXAMPLE_VALUE "Test message EXAMPLE_VALUE from example-module-file version 0.2"
+
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/dls-pmac-control/0.2/entrypoints"
diff --git a/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec
new file mode 100755
index 0000000..02556e4
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts="/dls/science/users/:/dls/science/users/,/scratch:/scratch,/dls_sw/apps:/dls_sw/apps"
+# Additional arguments for apptainer
+apptainer_args=""
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/4b34247055f8388a8877c90302ff30d2.sif"
+# Command to run in container
+command="ec"
+# Options and arguments to pass to command
+command_args=""
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in kubectl helm kubelogin klogout kustomize kubeseal kubectl-oidc_login; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-bash b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-bash
new file mode 100755
index 0000000..35c7727
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-bash
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts="/dls/science/users/:/dls/science/users/,/scratch:/scratch,/dls_sw/apps:/dls_sw/apps"
+# Additional arguments for apptainer
+apptainer_args=""
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/4b34247055f8388a8877c90302ff30d2.sif"
+# Command to run in container
+command="bash"
+# Options and arguments to pass to command
+command_args=""
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in kubectl helm kubelogin klogout kustomize kubeseal kubectl-oidc_login; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-login b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-login
new file mode 100755
index 0000000..b150b79
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints/ec-login
@@ -0,0 +1,7 @@
+#! /bin/bash
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
+argocd login argocd.diamond.ac.uk --grpc-web --sso
diff --git a/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/module.yaml b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/module.yaml
new file mode 100644
index 0000000..6b563eb
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/module.yaml
@@ -0,0 +1,52 @@
+applications:
+- app_type: apptainer
+  container:
+    path: docker://ghcr.io/epics-containers/edge-containers-cli
+    version: 4.4.1
+  entrypoints:
+  - command: ec
+    name: ec
+    options:
+      apptainer_args: ''
+      command_args: ''
+      host_binaries: []
+      mounts: []
+  - command: bash
+    name: ec-bash
+    options:
+      apptainer_args: ''
+      command_args: ''
+      host_binaries: []
+      mounts: []
+  global_options:
+    apptainer_args: ''
+    command_args: ''
+    host_binaries:
+    - kubectl
+    - helm
+    - kubelogin
+    - klogout
+    - kustomize
+    - kubeseal
+    - kubectl-oidc_login
+    mounts:
+    - /dls/science/users/:/dls/science/users/
+    - /scratch:/scratch
+    - /dls_sw/apps:/dls_sw/apps
+- app_type: shell
+  name: ec-login
+  script:
+  - argocd login argocd.diamond.ac.uk --grpc-web --sso
+dependencies: []
+description: ec command line tool for kubernetes IOCs
+env_vars:
+- name: EC_CLI_BACKEND
+  value: K8S
+- name: EC_LOG_URL
+  value: https://graylog.diamond.ac.uk/search?rangetype=relative&fields=message%2Csource&width=1489&highlightMessage=&relative=172800&q=pod_name%3A{service_name}*
+- name: EC_TARGET
+  value: p47-beamline
+- name: EC_SERVICES_REPO
+  value: https://github.com/epics-containers/p47-services
+name: edge-containers-cli
+version: '0.1'
diff --git a/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/modulefile b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/modulefile
new file mode 100644
index 0000000..a5fe676
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/edge-containers-cli/0.1/modulefile
@@ -0,0 +1,13 @@
+#%Module1.0
+##
+## edge-containers-cli - ec command line tool for kubernetes IOCs
+##
+module-whatis "ec command line tool for kubernetes IOCs"
+
+setenv EC_CLI_BACKEND "K8S"
+setenv EC_LOG_URL "https://graylog.diamond.ac.uk/search?rangetype=relative&fields=message%2Csource&width=1489&highlightMessage=&relative=172800&q=pod_name%3A{service_name}*"
+setenv EC_TARGET "p47-beamline"
+setenv EC_SERVICES_REPO "https://github.com/epics-containers/p47-services"
+
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/edge-containers-cli/0.1/entrypoints"
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/cowsay-hello b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/cowsay-hello
new file mode 100755
index 0000000..8e6480e
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/cowsay-hello
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts="/dls_sw:/dls_sw_test:ro"
+# Additional arguments for apptainer
+apptainer_args=""
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/a553018b87553334a94c33cb04eb025c.sif"
+# Command to run in container
+command="cowsay"
+# Options and arguments to pass to command
+command_args="Hello"
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in ; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/show-directory b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/show-directory
new file mode 100755
index 0000000..111f5a5
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/show-directory
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts="/dls_sw:/dls_sw_test:ro"
+# Additional arguments for apptainer
+apptainer_args=""
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/a553018b87553334a94c33cb04eb025c.sif"
+# Command to run in container
+command="ls"
+# Options and arguments to pass to command
+command_args="-al /dls_sw_test"
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in ; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-echo-module-folder b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-echo-module-folder
new file mode 100755
index 0000000..0a367dd
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-echo-module-folder
@@ -0,0 +1,7 @@
+#! /bin/bash
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
+echo $OTHER_VALUE
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-shell-script b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-shell-script
new file mode 100755
index 0000000..6ca6871
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/entrypoints/test-shell-script
@@ -0,0 +1,9 @@
+#! /bin/bash
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+
+echo This is the first line of a shell script
+echo and this is the second line.
+echo Your input is ${1}
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/module.yaml b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/module.yaml
new file mode 100644
index 0000000..496c098
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/module.yaml
@@ -0,0 +1,43 @@
+applications:
+- app_type: apptainer
+  container:
+    path: docker://ghcr.io/apptainer/lolcow
+    version: latest
+  entrypoints:
+  - command: cowsay
+    name: cowsay-hello
+    options:
+      apptainer_args: ''
+      command_args: Hello
+      host_binaries: []
+      mounts: []
+  - command: ls
+    name: show-directory
+    options:
+      apptainer_args: ''
+      command_args: -al /dls_sw_test
+      host_binaries: []
+      mounts: []
+  global_options:
+    apptainer_args: ''
+    command_args: ''
+    host_binaries: []
+    mounts:
+    - /dls_sw:/dls_sw_test:ro
+- app_type: shell
+  name: test-echo-module-folder
+  script:
+  - echo $OTHER_VALUE
+- app_type: shell
+  name: test-shell-script
+  script:
+  - echo This is the first line of a shell script
+  - echo and this is the second line.
+  - echo Your input is ${1}
+dependencies: []
+description: Demonstration of a module configuration folder
+env_vars:
+- name: OTHER_VALUE
+  value: Test message OTHER_VALUE from example-module-folder
+name: example-module-apps
+version: '0.1'
diff --git a/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/modulefile b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/modulefile
new file mode 100644
index 0000000..56623f3
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-apps/0.1/modulefile
@@ -0,0 +1,10 @@
+#%Module1.0
+##
+## example-module-apps - Demonstration of a module configuration folder
+##
+module-whatis "Demonstration of a module configuration folder"
+
+setenv OTHER_VALUE "Test message OTHER_VALUE from example-module-folder"
+
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/example-module-apps/0.1/entrypoints"
diff --git a/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/module.yaml b/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/module.yaml
new file mode 100644
index 0000000..7763904
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/module.yaml
@@ -0,0 +1,10 @@
+applications: []
+dependencies:
+- name: dls-pmac-control
+  version: '0.1'
+- name: example-module-apps
+  version: '0.1'
+description: Demonstration of deploy-tools dependencies
+env_vars: []
+name: example-module-deps
+version: '0.2'
diff --git a/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/modulefile b/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/modulefile
new file mode 100644
index 0000000..0c553eb
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/example-module-deps/0.2/modulefile
@@ -0,0 +1,11 @@
+#%Module1.0
+##
+## example-module-deps - Demonstration of deploy-tools dependencies
+##
+module-whatis "Demonstration of deploy-tools dependencies"
+
+
+module load dls-pmac-control/0.1
+module load example-module-apps/0.1
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/example-module-deps/0.2/entrypoints"
diff --git a/tests/samples/deploy-tools-output/modules/phoebus/0.1/entrypoints/phoebus b/tests/samples/deploy-tools-output/modules/phoebus/0.1/entrypoints/phoebus
new file mode 100755
index 0000000..0dc0fef
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/phoebus/0.1/entrypoints/phoebus
@@ -0,0 +1,44 @@
+#! /bin/bash
+
+# Arguments:
+# ${@} = Remaining args to pass to the command
+
+# Halt on error
+set -e
+
+# Mounts for container
+mounts=""
+# Additional arguments for apptainer
+apptainer_args="--env DISPLAY=${DISPLAY} -e"
+# Sif file path
+sif_file="$(dirname $0)/../sif_files/433dd7c0f3803fb792bf46b323938691.sif"
+# Command to run in container
+command="java -jar /phoebus/phoebus.jar -server 7010"
+# Options and arguments to pass to command
+command_args="-server 7010"
+
+# Raise an error if sif file does not exist
+if [[ ! -f ${sif_file} ]]; then
+    echo "ERROR: sif file ${sif_file} does not exist" 1>&2
+    exit 1
+fi
+
+# add mounts of host binaries into /usr/bin
+for i in ; do
+    binary=$(which $i)
+    mounts="${mounts},${binary}:/usr/bin/${i}"
+done
+
+# Set up mounts if any have been configured
+if [[ ! -z ${mounts} ]]; then
+    opts="-B ${mounts}"
+fi
+
+opts=${opts}" --env DISPLAY=${DISPLAY}"
+opts=${opts}" ${apptainer_args}"
+
+
+if [[ -n "${DEPLOY_TOOLS_VERBOSE}" ]]; then
+    set -x
+fi
+apptainer exec ${opts} ${sif_file} ${command} ${command_args} "${@}"
diff --git a/tests/samples/deploy-tools-output/modules/phoebus/0.1/module.yaml b/tests/samples/deploy-tools-output/modules/phoebus/0.1/module.yaml
new file mode 100644
index 0000000..c793ed1
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/phoebus/0.1/module.yaml
@@ -0,0 +1,23 @@
+applications:
+- app_type: apptainer
+  container:
+    path: docker://ghcr.io/epics-containers/ec-phoebus
+    version: 4.7.3ec2
+  entrypoints:
+  - command: java -jar /phoebus/phoebus.jar -server 7010
+    name: phoebus
+    options:
+      apptainer_args: --env DISPLAY=${DISPLAY} -e
+      command_args: -server 7010
+      host_binaries: []
+      mounts: []
+  global_options:
+    apptainer_args: ''
+    command_args: ''
+    host_binaries: []
+    mounts: []
+dependencies: []
+description: Containerised release of CSS Phoebus
+env_vars: []
+name: phoebus
+version: '0.1'
diff --git a/tests/samples/deploy-tools-output/modules/phoebus/0.1/modulefile b/tests/samples/deploy-tools-output/modules/phoebus/0.1/modulefile
new file mode 100644
index 0000000..29810fb
--- /dev/null
+++ b/tests/samples/deploy-tools-output/modules/phoebus/0.1/modulefile
@@ -0,0 +1,9 @@
+#%Module1.0
+##
+## phoebus - Containerised release of CSS Phoebus
+##
+module-whatis "Containerised release of CSS Phoebus"
+
+
+
+prepend-path PATH "/tmp/deploy-tools-output/modules/phoebus/0.1/entrypoints"
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 745afdd..31e378a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,9 +1,56 @@
 import subprocess
 import sys
+import tempfile
+from pathlib import Path
+from shutil import rmtree
 
+from conftest import run_cli
 from deploy_tools import __version__
 
 
 def test_cli_version():
     cmd = [sys.executable, "-m", "deploy_tools", "--version"]
     assert subprocess.check_output(cmd).decode().strip() == __version__
+
+
+def test_schema(schemas: Path):
+    with tempfile.TemporaryDirectory() as tmp:
+        tmp_path = Path(tmp)
+
+        # Generate up to date schema files
+        run_cli("schema", tmp_path)
+
+        # Compare with the expected schema files
+        for schema in tmp_path.glob("*.json"):
+            expected = schemas / schema.name
+            if schema.read_text() != expected.read_text():
+                raise AssertionError(f"Schema file {expected} is out of date.")
+
+
+def test_demo_configuration(samples: Path, demo_config: Path):
+    # use a fixed path for the demo configuration so that the outputs are consistent
+    out_folder = "deploy-tools-output"
+    temp_out = Path("/tmp") / out_folder
+    expected_out = samples / out_folder
+
+    # make sure the output directory is empty and exists
+    rmtree(temp_out, ignore_errors=True)
+    temp_out.mkdir(exist_ok=True)
+
+    # generate the demo configuration output
+    run_cli("sync", "--from-scratch", str(temp_out), str(demo_config))
+
+    # compare the output with the expected output
+    for expected in expected_out.glob("**/*"):
+        if expected.is_dir():
+            continue
+        # check that the file exists in the output directory
+        out_file = temp_out / expected.relative_to(expected_out)
+        assert out_file.exists(), f"File {out_file} does not exist."
+
+        # check that the file contents are the same
+        assert expected.read_text() == out_file.read_text(), (
+            f"File {out_file} is different."
+        )
+
+    rmtree(temp_out, ignore_errors=True)