publication . Article . 2015

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

Alastair P. Droop;
Open Access English
  • Published: 03 Dec 2015 Journal: Bioinformatics, volume 32, issue 8, pages 1,267-1,268 (issn: 1367-4803, eissn: 1367-4811, Copyright policy)
  • Publisher: Oxford University Press
Abstract
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-...
Subjects
free text keywords: Applications Notes, Data and Text Mining, Workflow, Scripting language, computer.software_genre, computer, Interpreter, Data mining, Computing Methodologies, Computer science, Bioinformatics analysis, Bioinformatics, Process logic, Grid, Software, business.industry, business
Related Organizations

Deelman E. (2009) Workflows and e-Science: an overview of workflow system features and capabilities. Futur. Gen. Comp. Syst., 25, 528–540. [OpenAIRE]

Deelman E. (2015) Pegasus, a workflow management system for science automation. Futur. Gen. Comp. Syst., 46, 17–35. [OpenAIRE]

Giardine B. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451–1455.16169926 [OpenAIRE] [PubMed]

Li H.Durbin R. (2009) Fast and accurate short read alignment with Burrows–Wheeler Transform. Bioinformatics, 25, 1754–1760.19451168 [OpenAIRE] [PubMed]

Oinn T. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 20, 3045–3054.15201187 [OpenAIRE] [PubMed]

Wolstencroft K. (2013) The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res., 41, W557–W561.23640334 [OpenAIRE] [PubMed]

Abstract
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-...
Subjects
free text keywords: Applications Notes, Data and Text Mining, Workflow, Scripting language, computer.software_genre, computer, Interpreter, Data mining, Computing Methodologies, Computer science, Bioinformatics analysis, Bioinformatics, Process logic, Grid, Software, business.industry, business
Related Organizations

Deelman E. (2009) Workflows and e-Science: an overview of workflow system features and capabilities. Futur. Gen. Comp. Syst., 25, 528–540. [OpenAIRE]

Deelman E. (2015) Pegasus, a workflow management system for science automation. Futur. Gen. Comp. Syst., 46, 17–35. [OpenAIRE]

Giardine B. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451–1455.16169926 [OpenAIRE] [PubMed]

Li H.Durbin R. (2009) Fast and accurate short read alignment with Burrows–Wheeler Transform. Bioinformatics, 25, 1754–1760.19451168 [OpenAIRE] [PubMed]

Oinn T. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 20, 3045–3054.15201187 [OpenAIRE] [PubMed]

Wolstencroft K. (2013) The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res., 41, W557–W561.23640334 [OpenAIRE] [PubMed]

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publication . Article . 2015

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

Alastair P. Droop;