Florian Eggenhofer

Development of Architecture for Software Containers - practical computational reproducibility for everyone

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

  • a repository of recipes hosted on GitHub
  • a build system that turns these recipes into conda packages
  • a repository of more than 3000 bioinformatics packages ready to use with conda install
  • over 250 contributors that add, modify, update and maintain the recipes

The conda package manager makes 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 and other programs on Linux, Mac OSX, and Windows.

Conda allows separation of packages into repositories, or channels. The main defaults channel has a large number of common packages. Users can add additional channels from which to install software packages not available in the defaults channel. Bioconda is one such channel specializing in bioinformatics software.

Each package added to Bioconda also has a corresponding Docker BioContainer automatically created and uploaded to Quay.io.

Short CV

Dr. Florian Eggenhofer received his doctoral degree from the University of Vienna, Austria, and is now a postdoctoral researcher at the University of Freiburg. He is an active contributor of the bioconda project.