skip to navigation
skip to content

Not Logged In

bioscons 0.7

Functions extending the scons build tool for reproducible research in bioinformatics.

Latest Version: 0.8.1

This package extends the scons build tool for the construction of reproducible workflows in bioinformatics.

This project is in fairly early stages of development, although I have been using scons to create workflows using an earlier version of this package for some time.

Background

Why does SCons make sense for reproducible bioinformatics pipelines?

  • SCons has a sophisticated mechanism for determining dependencies, meaning that re-running SCons will only re-execute steps needing updating
  • Most of the work of pipelines is done by external programs, and SCons is explicitly designed to make it easy to run external programs
  • On the other hand, SCons also allows the execution of arbitrary python code in creating your script, and thus one can leverage the power of the python standard library, Biopython, NumPy, etc in your script.
  • Rather than dealing with a mess of filenames, subsequent steps in an SCons build are expressed in terms of file objects
  • Steps in the pipeline are implemented using objects called “builders,” which implement a shell command or a python command in a in a way that consistently channels inputs into outputs
  • Provides multiple mechanisms for cleanly executing isolated steps of the workflow
  • SCons validates files and can fail incrementally

Alternative tools

make
Make is a classic and everywhere, but getting make to do complex things requires specialized (and often opaque) syntax
ruffus
ruffus is a lightweight way to automate bioinformatics pipelines. It also supports incremental recalculation. It does not, however, provide assistance for executing shell commands or managing files, and these must be done with explict sytem calls on “hand-built” strings.
galaxy
galaxy is a web-based tool for building remotely-executed workflows. This is a hugely attractive framework for exposing complex workflows using a graphical-interface, but occupies a very different niche from this project (which provides a command line interface to locally-executed programs).

Documentation

Documentation is available on github: http://nhoffman.github.com/bioscons/

Installation

PyPi

Make sure to update the __version__ variable in the bioscons/__init__.py file.

If you have not done so create a ~/.pypirc file:

python setup.py register

Proceed to build and upload:

python setup.py clean
python setup.py sdist bdist_wheel
twine upload dist/*

dependencies

scons

Development of this project begin using the 1.x version of scons, and seems to work so far using version 2.x. Future development will focus on version 2.x.

source

Obtain the source code from github. For read-only access:

git clone git://github.com/nhoffman/bioscons.git

For committers:

git clone git@github.com:nhoffman/bioscons.git

Then install:

cd bioscons
python setup.py install
 
File Type Py Version Uploaded on Size
bioscons-0.7-py2-none-any.whl (md5) Python Wheel py2 2014-06-10 24KB
bioscons-0.7.tar.gz (md5) Source 2014-06-10 19KB
  • Downloads (All Versions):
  • 6 downloads in the last day
  • 194 downloads in the last week
  • 765 downloads in the last month