qsubsec: a lightweight template system for defining sun grid engine workflows.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 26635140.
- Also identified by DOI 10.1093/bioinformatics/btv698 and PMC identifier 4824124.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Computational Biology
- Computing Methodologies
- Software