diff --git a/README.md b/README.md
index 026950c..ab45807 100644
--- a/README.md
+++ b/README.md
@@ -112,16 +112,31 @@ Used when `VECTOR_DB_TYPE=qdrant`.
 * `QDRANT_PORT`: Port of the Qdrant service (default: `6333`).
 * `QDRANT_COLLECTION`: Name of the Qdrant collection.
 
-## Vectorstore Visualization
-Running `poetry run python visualize.py` will generate a 2d scatterplot
-of the vectors.
-See `visualize.ChartType` for supported charts.
+## RAG Pipeline Invocation
+The ZenML RAG pipeline can be invoked using the `run-pipeline` script. This script allows for running different parts of the pipeline with various configurations.
 
-![image](scatterplot2d.png)
+### Configuration
+Local runs should include a `.env` file in the project root to load necessary environment variables.
+
+### Local Execution
+To run the feature engineering pipeline locally:
+```shell
+poetry run run-pipeline --run-feature-engineering
+```
 
-![image](scatterplot3d.png)
+To run without caching:
+```shell
+poetry run run-pipeline --run-feature-engineering --no-cache
+```
 
-# Gemini Agent Configuration
+Available options:
+- `--no-cache`: Disable ZenML caching.
+- `--run-feature-engineering`: Run the feature engineering pipeline.
+- `--run-end-to-end-data`: Run the full data pipeline.
+- ... (see `poetry run run-pipeline --help` for all options)
+
+### Unit Tests
+...
 
 The `gemeni` directory contains the configuration files for the Gemini agent.
 
diff --git a/docs/Agent-Devops.md b/docs/agent/Agent-Devops.md
similarity index 100%
rename from docs/Agent-Devops.md
rename to docs/agent/Agent-Devops.md
diff --git a/docs/Agent.md b/docs/agent/Agent.md
similarity index 85%
rename from docs/Agent.md
rename to docs/agent/Agent.md
index 1f551c1..d485f42 100644
--- a/docs/Agent.md
+++ b/docs/agent/Agent.md
@@ -1,5 +1,5 @@
 # System Prompt
-You are an expert Software Engineer, who specializes in `Python`, `Docker`, `zenml`, and RAG Data Pipelines.
+You are an expert Software Engineer, who specializes in `Python`, `Docker`, `mongo`, `zenml`, and RAG Data Pipelines.
 
 You always enter plan mode.
 
@@ -15,9 +15,6 @@ For this project, you are working on a RAG feature pipeline, which will
 - Clean data from the data lake.
 - Chunk and embed in the vector store.
 
-# User Prompt
-Please wait for user input.
-
 ## Development Tools
 ### Tox
 This project includes `tox`. Its purpose is
@@ -50,3 +47,14 @@ The service runs locally on the `babylon` docker-compose network, in which the f
 - Vector DB: Name: `chroma`
 - Secrets Manager: Name: `openbao`
 - ZenML Orchestrator: Name: `zenml`
+
+
+# User Prompt
+Please wait for user input.
+
+## Planning
+When planning, write your plan to `<GIT_BRANCH_NAME>.md`, where `<GIT_BRANCH_NAME>` is the name of the current local git branch.
+Ask the user to validate the plan before executing.
+
+## Readme
+Always keep the `README.md` up-to-date with relevant information.
diff --git a/docs/Zenml-Integration.md b/docs/agent/Zenml-Integration.md
similarity index 100%
rename from docs/Zenml-Integration.md
rename to docs/agent/Zenml-Integration.md
diff --git a/docs/agent/run-features.md b/docs/agent/run-features.md
new file mode 100644
index 0000000..36f0ead
--- /dev/null
+++ b/docs/agent/run-features.md
@@ -0,0 +1,20 @@
+We are updating `tools/run.py` so that `features` generation can be invoked.
+
+## Python Application Configuration Settings
+- Python Application Configuration settings should exist in `.env` for local runs.
+
+## ZenML Pipeline Infrastructure Configuration
+- zenml infrastructure configuration exists in `./zenml/pipeline/config`.
+
+### ZenML Docker Image.
+- The pipeline configuration should point to the image created by `Dockerfile`. For now it's only a locally built image.
+
+## Task
+Your task is to ensure that `poetry run run.py` correctly invokes `generate_features` via Zenml.
+Note that some implementation details are still in progress. Create mock data where appropriate.
+
+## Validation
+To validate your changes, build a `tests/test_run.py` pytest suite.
+
+## Open Questions
+Write any open questions to a file `QUESTIONS.md`. Wait for the user to respond before executing.
diff --git a/docs/upload-artifact.md b/docs/agent/upload-artifact.md
similarity index 100%
rename from docs/upload-artifact.md
rename to docs/agent/upload-artifact.md
diff --git a/features/pipeline/generate_features.py b/features/pipeline/generate_features.py
index be00237..cc031fb 100644
--- a/features/pipeline/generate_features.py
+++ b/features/pipeline/generate_features.py
@@ -7,9 +7,13 @@
 
 
 @pipeline
-def generate_features(wait_for: str | list[str] | None = None) -> list[str]:
+def generate_features(
+    wait_for: str | list[str] | None = None,
+    mock: bool = False,
+    **kwargs,
+) -> list[str]:
     """Entry point to the zenml pipeline for generating Babylon features."""
-    raw_documents = fg_steps.query_data_lake(after=wait_for)
+    raw_documents = fg_steps.query_data_lake(after=wait_for, mock=mock)
     clean_documents = fg_steps.clean_documents(raw_documents)
 
     # Load cleaned docs to vector db.
diff --git a/features/steps/feature_generation/query_data_lake.py b/features/steps/feature_generation/query_data_lake.py
index 230aae5..e4f94f6 100644
--- a/features/steps/feature_generation/query_data_lake.py
+++ b/features/steps/feature_generation/query_data_lake.py
@@ -10,11 +10,18 @@
 @step
 def query_data_lake(
     transaction_descriptions: list[str] | None = None,
+    mock: bool = False,
 ) -> Annotated[list, "raw_documents"]:
     """Entry point to query the datalake for new documents.
 
-    :param transaction_descriptions: Optional list of
+    :param transaction_descriptions: Optional list of transaction descriptions.
+    :param mock: Whether to return mock data.
     """
+    if mock:
+        return [
+            {"id": "1", "content": "Sample transaction 1", "metadata": {"source": "mock"}},
+            {"id": "2", "content": "Sample transaction 2", "metadata": {"source": "mock"}},
+        ]
     documents: list = []
     # todo
     return documents
diff --git a/features/tools/__init__.py b/features/tools/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/features/tools/run.py b/features/tools/run.py
new file mode 100644
index 0000000..6464047
--- /dev/null
+++ b/features/tools/run.py
@@ -0,0 +1,175 @@
+"""
+Driver script for invoking the Zenml RAG pipeline.
+This script will be updated accordingly as more steps are built.
+"""
+from datetime import datetime as dt
+from pathlib import Path
+
+import click
+import dotenv
+from loguru import logger
+
+from features.config import config
+
+from features.pipeline import (
+    generate_features,
+)
+
+_HELP_PROMPT = """
+Babylon RAG Pipeline.
+
+Main entry point for pipeline execution.
+
+Run the Run the ZenML project pipelines with various options.
+
+Run a pipeline with the required parameters. This executes
+all steps in the pipeline in the correct order using the orchestrator
+stack component that is configured in your active ZenML stack.
+
+Examples:
+    \b
+    # Run the pipeline with default options
+    python run.py
+    
+    \b
+    # Run the pipeline without cache
+    python run.py --no-cache
+    
+    \b
+    # Run only the ETL pipeline
+    python run.py --only-etl
+"""
+@click.command(
+    help=_HELP_PROMPT
+)
+@click.option(
+    "--no-cache",
+    is_flag=True,
+    default=False,
+    help="Disable caching for the pipeline run.",
+)
+@click.option(
+    "--run-end-to-end-data",
+    is_flag=True,
+    default=False,
+    help="Whether to run all the data pipelines in one go.",
+)
+@click.option(
+    "--run-etl",
+    is_flag=True,
+    default=False,
+    help="Whether to run the ETL pipeline.",
+)
+@click.option(
+    "--run-export-artifact-to-json",
+    is_flag=True,
+    default=False,
+    help="Whether to run the Artifact -> JSON pipeline",
+)
+@click.option(
+    "--etl-config-filename",
+    default="digital_data_etl_paul_iusztin.yaml",
+    help="Filename of the ETL config file.",
+)
+@click.option(
+    "--run-feature-engineering",
+    is_flag=True,
+    default=False,
+    help="Whether to run the FE pipeline.",
+)
+@click.option(
+    "--run-generate-instruct-datasets",
+    is_flag=True,
+    default=False,
+    help="Whether to run the instruct dataset generation pipeline.",
+)
+@click.option(
+    "--run-generate-preference-datasets",
+    is_flag=True,
+    default=False,
+    help="Whether to run the preference dataset generation pipeline.",
+)
+@click.option(
+    "--run-training",
+    is_flag=True,
+    default=False,
+    help="Whether to run the training pipeline.",
+)
+@click.option(
+    "--run-evaluation",
+    is_flag=True,
+    default=False,
+    help="Whether to run the evaluation pipeline.",
+)
+@click.option(
+    "--export-settings",
+    is_flag=True,
+    default=False,
+    help="Whether to export your settings to ZenML or not.",
+)
+def main(
+    no_cache: bool = False,
+    run_end_to_end_data: bool = False,
+    run_etl: bool = False,
+    run_export_artifact_to_json: bool = False,
+    etl_config_filename: str = "digital_data_etl_paul_iusztin.yaml",
+    run_feature_engineering: bool = False,
+    run_generate_instruct_datasets: bool = False,
+    run_generate_preference_datasets: bool = False,
+    run_training: bool = False,
+    run_evaluation: bool = False,
+    export_settings: bool = False,
+):
+    if not any(
+        [
+            run_feature_engineering,
+            run_end_to_end_data,
+            run_etl,
+            run_generate_instruct_datasets,
+            run_generate_preference_datasets,
+            run_training,
+            run_evaluation,
+        ]
+    ):
+        click.echo("Please specify an action to run.")
+        return
+
+    pipeline_args = {
+        "enable_cache": not no_cache,
+    }
+    # root_dir is two levels up from features/tools/run.py
+    root_dir = Path(__file__).resolve().parent.parent.parent
+    logger.debug(f"Project root directory: {root_dir}")
+
+    if run_feature_engineering:
+        # Features pipeline config.
+        run_args_fe = {}
+        # Update environment with any `.env` (for local runs only)
+        env_path = root_dir / ".env"
+        if env_path.exists():
+            logger.info(f"Update environment with `{env_path}`")
+            dotenv.load_dotenv(env_path)
+        else:
+            logger.warning(f"No .env found at {env_path}")
+
+        # Update config with existing environment variables.
+        logger.debug("Loading features config with environment variables.")
+        config.update_config_from_environment(run_args_fe)
+        logger.info("Environment loaded.")
+
+        pipeline_args["config_path"] = (
+            root_dir / "zenml" / "pipeline" / "config" / "feature_engineering.yaml"
+        )
+        pipeline_args["run_name"] = (
+            f"feature_engineering_run_{dt.now().strftime('%Y_%m_%d_%H_%M_%S')}"
+        )
+
+        logger.info(f"Invoking generate_features with config {pipeline_args['config_path']}")
+        generate_features.with_options(**pipeline_args)(**run_args_fe)
+
+    else:
+        logger.warning("Selected action is not yet implemented in run.py.")
+
+
+if __name__ == '__main__':
+    main()
diff --git a/pyproject.toml b/pyproject.toml
index a730ce1..c367864 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,6 +37,9 @@ matplotlib = "^3.10.7"
 plotly = "^6.3.1"
 scikit-learn = "1.7.2"
 
+[tool.poetry.scripts]
+run-pipeline = "features.tools.run:main"
+
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
diff --git a/tests/test_run.py b/tests/test_run.py
new file mode 100644
index 0000000..6b8cd43
--- /dev/null
+++ b/tests/test_run.py
@@ -0,0 +1,61 @@
+import sys
+from pathlib import Path
+from unittest.mock import patch, MagicMock
+import pytest
+from click.testing import CliRunner
+
+# Add the project root to sys.path if needed
+sys.path.append(str(Path(__file__).resolve().parent.parent))
+
+from features.tools.run import main
+
+def test_main_help():
+    """Test that the help message is displayed."""
+    runner = CliRunner()
+    result = runner.invoke(main, ["--help"])
+    assert result.exit_code == 0
+    assert "Babylon RAG Pipeline." in result.output
+
+@patch("features.tools.run.dotenv.load_dotenv")
+@patch("features.tools.run.config.update_config_from_environment")
+@patch("features.tools.run.generate_features")
+def test_main_run_feature_engineering(mock_generate_features, mock_update_config, mock_load_dotenv):
+    """Test that run_feature_engineering calls the pipeline with expected config."""
+    # Setup mocks
+    mock_pipeline_with_options = MagicMock()
+    mock_generate_features.with_options.return_value = mock_pipeline_with_options
+    
+    # We need to simulate that some env vars are found and populated into run_args_fe
+    def side_effect(config_dict):
+        config_dict["MOCK_CONFIG"] = "MOCK_VALUE"
+    mock_update_config.side_effect = side_effect
+
+    runner = CliRunner()
+    # We need to pass --run-feature-engineering
+    result = runner.invoke(main, ["--run-feature-engineering"])
+    
+    # Assertions
+    assert result.exit_code == 0
+    
+    # Check if load_dotenv was called (assuming .env might exist in test environment or we mock it)
+    # Even if it doesn't exist, we check if it was attempted.
+    assert mock_load_dotenv.called
+    
+    # Check if generate_features.with_options was called
+    assert mock_generate_features.with_options.called
+    options_call_args = mock_generate_features.with_options.call_args[1]
+    assert "config_path" in options_call_args
+    assert "feature_engineering.yaml" in str(options_call_args["config_path"])
+    
+    # Check if the pipeline was invoked with run_args_fe
+    mock_pipeline_with_options.assert_called_once()
+    invocation_args = mock_pipeline_with_options.call_args[1]
+    assert invocation_args["MOCK_CONFIG"] == "MOCK_VALUE"
+
+def test_main_no_action():
+    """Test that main shows an error if no action is specified."""
+    runner = CliRunner()
+    result = runner.invoke(main, [])
+    # In the updated run.py, it logs an error and returns instead of asserting
+    # logger.error("Please specify an action to run.")
+    assert "Please specify an action to run." in result.output
diff --git a/zenml/pipeline/config/end_to_end_data.yml b/zenml/pipeline/config/end_to_end_data.yml
new file mode 100644
index 0000000..f78b066
--- /dev/null
+++ b/zenml/pipeline/config/end_to_end_data.yml
@@ -0,0 +1,16 @@
+settings:
+  docker:
+    # todo: this should be the image built by babylon.
+    # parent_image: 992382797823.dkr.ecr.eu-central-1.amazonaws.com/zenml-rlwlcs:latest
+    skip_build: True
+  orchestrator.sagemaker:
+    synchronous: false
+
+parameters:
+  # Data ETL & Feature engineering pipelines parameters
+  # Add config as needed
+  # Generate instruct dataset pipeline parameters
+  test_split_size: 0.1
+  push_to_huggingface: false
+  dataset_id: 'todo'
+  mock: false
\ No newline at end of file
diff --git a/zenml/pipeline/config/feature_engineering.yaml b/zenml/pipeline/config/feature_engineering.yaml
new file mode 100644
index 0000000..726f5da
--- /dev/null
+++ b/zenml/pipeline/config/feature_engineering.yaml
@@ -0,0 +1,16 @@
+settings:
+  docker:
+    # This image is built by babylon-features.
+    parent_image: babylon-features:latest
+    skip_build: True
+  orchestrator:
+    synchronous: true
+
+parameters:
+  # Data ETL & Feature engineering pipelines parameters
+  # Add config as needed
+  # Generate instruct dataset pipeline parameters
+  test_split_size: 0.1
+  push_to_huggingface: false
+  dataset_id: 'todo'
+  mock: true