Complex heterogeneous dynamic networks like knowledge graphs are powerful constructs that can be used in modeling data provenance from computer systems. From a security perspective, these attributed graphs enable causality analysis and tracing for analyzing a myriad of cyberattacks. However, there is a paucity in systematic development of pipelines that transform system executions and provenance into usable graph representations for machine learning tasks. This lack of instrumentation severely inhibits scientific advancement in provenance graph machine learning by hindering reproducibility and limiting the availability of data that are critical for techniques like graph neural networks. To fulfill this need, we present Flurry, an end-to-end data pipeline which simulates cyberattacks, captures provenance data from these attacks at multiple system and application layers, converts audit logs from these attacks into data provenance graphs, and incorporates this data with a framework for training deep neural models that supports preconfigured or custom-designed models for analysis in real-world resilient systems. We showcase this pipeline by processing data from multiple system attacks and performing anomaly detection via graph classification using current benchmark graph representational learning frameworks. Flurry provides a fast, customizable, extensible, and transparent solution for providing this much needed data to cybersecurity professionals.