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Bioinformatics. 2013 Feb 1;29(3):387-8. doi: 10.1093/bioinformatics/bts696. Epub 2012 Dec 6.

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

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  • 1Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.


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.


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).

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