Bioconda: A sustainable and comprehensive software distribution for the life sciences
bioRxiv (Cold Spring Harbor Laboratory)2017
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Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastián Luna-Valero, Rory Kirchner, Karel Břinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop–Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antão, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, Kévin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao‐Ou Zhang, Wei Shen, Jennifer Cabral, Cristel G. Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter Cock, Enrico Seiler, Colin Brislawn, Thi Hong Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimerà, Elmar Pruesse, Walter Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E. Larson, Matthew L. Workentine, Upendra Kumar Devisetty, Sacha Laurent, Pierrick Roger, Xavier Garnier, Rasmus Ågren, Aziz Khan, John M. Eppley, Wei Li, Bianca K. Stöcker, Tobias Rausch, James Taylor, Patrick R. Wright, Adam Taranto, Davide Chicco, Bengt Sennblad, Jasmijn A. Baaijens, Matthew Gopez, Nezar Abdennur, Iain Milne, Jens Preussner, Luca Pinello, Avi Srivastava, Aroon T. Chande, Philip Kensche, Yuri Pirola, Michael Knudsen, Ino de Bruijn, Kai Blin, Giorgio Gonnella, Oana M. Enache, Vivek Rai, Nicholas R. Waters, Saskia Hiltemann, Matthew L. Bendall, Christoph Stahl, Alistair Miles, Yannick Boursin, Yasset Pérez‐Riverol, Sebastian Schmeier, Erik Clarke, Kevin J. Arvai, Matthieu Jung, Tom ́as Di Domenico, Julien Seiler, Eric Rasche, Étienne Kornobis, Daniela Beißer, Sven Rahmann, Alexander S. Mikheyev, Camy Tran, Jordi Capellades, Christopher Schröder, Adrián Salatino, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster
Abstract
Abstract We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 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.
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