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Bioconda: A sustainable and comprehensive software distribution for the life sciences

 

Bioconda is a channel for the conda package manager specializing in bioinformatics software.

Bioconda supports only 64-bit Linux and Mac OSX.

Bioconda offers a collection of over 2900 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 250 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", doi.

Whilst there are a number of compilaions of Bioinformatics software, Bioconda looks to be by far the most comprehensive.

After installing Conda, the first step is to set up the Bioconda channel

conda config --add channels conda-forge
conda config --add channels bioconda

Packages can then be installed using

conda install cnvkit

This installs CNVkit plus the appropriate Python and R dependencies.


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