A simple, self-contained thread pool implementation for executing BLAST jobs in the background. It manages a fixed number of worker threads, a job queue, and provides start/shutdown lifecycle. The class is isolated (no internal dependencies beyond Ruby's Thread and Queue) and can be extracted for any Ruby project needing bounded concurrent task execution.

A utility class that recursively zips a directory into a ZIP file using the rubyzip gem. It handles directory traversal, file addition, and stream writing. The class is decoupled from the rest of the application and can be reused in any Ruby project requiring directory-to-ZIP conversion.

A JavaScript higher-order component (HOC) that wraps any chart class (e.g., Kablammo, HitsOverview, Circos) to add collapsible headers, SVG/PNG export buttons, and responsive redraw on window resize. It uses a consistent interface (static methods like canCollapse, name, className, graphId, dataName) and is independent of the specific chart implementation. This pattern can be extracted for any web project needing reusable chart wrappers with export functionality.

A utility module that executes shell commands with robust handling: forking, temp file redirection for stdout/stderr, PATH resolution, and environment variable control. It provides a clean Ruby interface for running external binaries (like BLAST+) and capturing output. The module has no internal dependencies and can be reused in any Ruby project requiring reliable subprocess execution.