title: qsubsec: a lightweight template system for defining sun grid engine workflows.
abstract: 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.
  
  
  
  Qsubsec is open-source and is available at https://github.com/alastair-droop/qsubsec
  
  
  
  a.p.droop@leeds.ac.uk
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: MRC Medical Bioinformatics Centre, University of Leeds, Clarendon Way, Leeds LS2 9NL, UK.
authors.forename: Alastair P
authors.initials: AP
authors.lastname: Droop
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003199:Computer Systems; D003205:Computing Methodologies; D012984:Software; D014584:User-Computer Interface; D057188:Workflow