  Motivation: Complex computational pipelines are becoming a staple of modern
scientific research. Often these pipelines are resource intensive and require
days of computing time. In such cases, it makes sense to run them over
distributed computer clusters where they can take advantage of the aggregated
resources of many powerful computers. In addition to this, researchers often
want to integrate their workflows into their own web servers. In these cases,
software is needed to manage the submission of jobs from the web interface to
the cluster and then return the results once the job has finished executing.
  Results: We have developed the Job Management System (JMS), a workflow
management system and interface for the Torque resource manager. The JMS
provides users with a user-friendly interface for creating complex workflows
with multiple stages. It integrates this workflow functionality with Torque, a
tool that is used to control and manage batch jobs on distributed computing
clusters. The JMS can be used by researchers to build and run complex
computational pipelines and provides functionality to include these pipelines
in external interfaces. The JMS is currently being used to house a number of
structural bioinformatics pipelines at the Research Unit in Bioinformatics
(RUBi) at Rhodes University.
  Availability: The JMS is an open-source project and is freely available at
https://github.com/RUBi-ZA/JMS
