Format

Send to

Choose Destination
See comment in PubMed Commons below
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.

Author information

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

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.

AVAILABILITY:

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).

PMID:
23220574
PMCID:
PMC3562064
DOI:
10.1093/bioinformatics/bts696
[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center