title: Nestly--a framework for running software with nested parameter choices and aggregating results.
abstract: 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.
  
  
  BACKGROUND
  Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).
authors.affiliation: Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. cmccoy@fhcrc.org
authors.forename: Connor O
authors.initials: CO
authors.lastname: McCoy
authors.forename: Aaron
authors.initials: A
authors.lastname: Gallagher
authors.forename: Noah G
authors.initials: NG
authors.lastname: Hoffman
authors.forename: Frederick A
authors.initials: FA
authors.lastname: Matsen
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D006801:Humans; D012984:Software