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Motivation: Complex computational pipelines are becoming a staple of modernscientific research. Often these pipelines are resource intensive and requiredays of computing time. In such cases, it makes sense to run them overdistributed computer clusters where they can take advantage of the aggregatedresources of many powerful computers. In addition to this, researchers oftenwant 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 tothe cluster and then return the results once the job has finished executing.  Results: We have developed the Job Management System (JMS), a workflowmanagement system and interface for the Torque resource manager. The JMSprovides users with a user-friendly interface for creating complex workflowswith multiple stages. It integrates this workflow functionality with Torque, atool that is used to control and manage batch jobs on distributed computingclusters. The JMS can be used by researchers to build and run complexcomputational pipelines and provides functionality to include these pipelinesin external interfaces. The JMS is currently being used to house a number ofstructural bioinformatics pipelines at the Research Unit in Bioinformatics(RUBi) at Rhodes University.  Availability: The JMS is an open-source project and is freely available athttps://github.com/RUBi-ZA/JMS

JMS: A workflow management system and web-based cluster front-end for the Torque resource manager