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Nestly--a framework for running software with nested parameter choices and aggregating results.

The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. AVAILABILITY: Source, documentation and tutorial examples are available at nestly can be installed from the Python Package Index via pip; it is open source (MIT license).

Pubmed ID: 23220574


  • McCoy CO
  • Gallagher A
  • Hoffman NG
  • Matsen FA


Bioinformatics (Oxford, England)

Publication Data

February 1, 2013

Associated Grants

  • Agency: NIAID NIH HHS, Id: R01 AI038518
  • Agency: NHGRI NIH HHS, Id: R01 HG005966-01

Mesh Terms

  • Algorithms
  • Computational Biology
  • Humans
  • Software