qsubsec: a lightweight template system for defining sun grid engine workflows

Summary: The Sun Grid Engine (SGE) high-performance computing batch queueing system is commonly used in bioinformatics analysis. Creating re-usable scripts for the SGE is a common challenge. The qsubsec template language and interpreter described here allow researchers to easily create generic template definitions that encapsulate a particular computational job, effectively separating the process logic from the specific run details. At submission time, the generic template is filled in with specific values. This system provides an intermediate level between simple scripting and complete workflow management tools. Availability and implementation: Qsubsec is open-source and is available at https://github.com/alastair-droop/qsubsec. Contact: a.p.droop@leeds.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.