1. Casey Dunn
  2. biolite

Overview

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BioLite is developed by the Dunn Lab at Brown University.

Quick Install

On 64-bit Linux, BioLite can be installed using prebuilt packages from our Anaconda channel. First, you will need to install the Anaconda distribution of Python. For a minimal install, you can for example install Miniconda in your home directory with:

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b
echo 'export "PATH=$HOME/miniconda2/bin:$PATH"' >>~/.bashrc
source ~/.bashrc

NOTE: by installing Miniconda with the -b option, you are acknowledging that you accept the terms of the Anaconda EULA from Continuum Analytics.

Once the conda command is in your PATH, BioLite can be installed into its own isolated conda environment with the single command:

conda create -c dunnlab -n biolite biolite

Once installed, activate the "biolite" conda environment with:

source activate biolite

We have primarily tested BioLite on CentOS 6.8 and Ubuntu 16.04, but in theory it should run on any Linux system with glibc >= 2.12.

See INSTALL for more detailed instructions, system requirements, and for how to configure BioLite after installing it.

Documentation

biolite.bitbucket.org

Background

BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines.

BioLite provides generalized components aimed at developers of NGS analyses workflows. These include:

  • a 'catalog' database for pairing metadata with and organizing NGS data files
  • a global 'diagnostics' database that establishes provenance for analyses and archives analysis results that can be accessed across multiple stages of a workflow, or from different workflows
  • a modular 'pipeline' framework with Python wrappers and workflows for commonly used NGS tools, and logging, profiling, and checkpointing functionality
  • a C++ library 'seqio' for efficient I/O of large NGS data files

Reporting Problems

Please use the issue tracker at Bitbucket to report and problems you have.

Updating and Uninstalling

BioLite is under active development. This means that new updates are not always compatiable with analyses that have already been run. We make every effort to avoid changes to the catalog database structure, so there is usually not a need to re-catalog data when you install a new version. However, you may need to rerun already completed analyses if you want to generate new reports or use existing data with new versions of pipelines.

If you installed BioLite with conda using the quick install instructions above, uninstall with:

conda env remove biolite

To upgrade a conda installation, use:

conda install -n biolite biolite

If you installed BioLite with pip, uninstall with:

pip uninstall biolite

To upgrade with pip, use:

pip install -U biolite

Citing

BioLite is still under development, and is an experimental tool that should be used with care. Please cite:

Howison M, Sinnott-Armstrong NA, Dunn CW. 2012. BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. In Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP '12), 14-15 June 2012, Boston, MA, USA.

BioLite makes use of many other programs that do much of the heavy lifting of the analyses. Please be sure to credit these essential components as well. Check the biolite.cfg file for web links to these programs, where you can find more information on how to cite them.

Funding

This software has been developed with support from the following US National Science Foundation grants:

PSCIC Full Proposal: The iPlant Collaborative: A Cyberinfrastructure-Centered Community for a New Plant Biology (Award Number 0735191)

Collaborative Research: Resolving old questions in Mollusc phylogenetics with new EST data and developing general phylogenomic tools (Award Number 0844596)

Infrastructure to Advance Life Sciences in the Ocean State (Award Number 1004057)

The Brown University Center for Computation and Visualization has been instrumental to the development of BioLite.

License

Copyright (c) 2012-2017 Brown University. All rights reserved.

BioLite is distributed under the GNU General Public License version 3. For more information, see LICENSE or visit: http://www.gnu.org/licenses/gpl.html

BioLite includes source code from the following projects:

  • gzstream C++ interface v1.5, which is distributed under the GNU Lesser General Public License in LICENSE.gzstream
  • Bootstrap v2.3.1 CSS style, which is distributed under the Apache License v2.0 in share/bootstrap.min.css
  • jsphylosvg v1.55, which is distributed under the GPL in LICENSE.jsphylosvg, and which includes Raphael 1.4.3, which is distributed under the MIT license
  • D3js v3.1.9, which is distributed under the BSD license in LICENSE.d3js
  • MersenneTwister C++ class, which distributed under the BSD license in tools/src/MersenneTwister.h