Bioconda: sustainable and comprehensive software distribution for the life sciences

作者：Ryan K. Dale, Björn A. Grüning, A. Sjödin, Jillian Rowe, Brad A. Chapman, C. Tomkins-Tinch, Renan Valieris, Bérénice Batut, A. Caprez, T. Cokelaer, Dilmurat Yusuf, K. Beauchamp, K. Břinda, Thomas Wollmann, Gildas Le Corguillé, D. Ryan, A. Bretaudeau, Y. Hoogstrate, Brent S. Pedersen, S. V. Heeringen, Martin Raden, Sebastian Luna-Valero, N. Soranzo, M. De Smet, G. von Kuster, Rory D. Kirchner, L. Pantano, Z. Charlop-Powers, Kevin R. Thornton, Marcel Martin, Marius van den Beek, Daniel Maticzka, Milad Miladi, S. Will, Kévin Gravouil, P. Unneberg, C. Brueffer, Clemens Blank, V. Piro, Joachim Wolff, T. Antao, Simon L. Gladman, I. Shlyakhter, M. de Hollander, P. Mabon, Wei Shen, J. Boekel, M. Holtgrewe, Dave Bouvier, J. D. de Ruiter, Jennifer Cabral, S. Choudhary, N. Harding, Robert Kleinkauf, E. Enns, Florian Eggenhofer, Joseph M Brown, P. Cock, H. Timm, Cristel G. Thomas, Xiao-Ou Zhang, Matt Chambers, Nitesh Turaga, E. Seiler, Colin J. Brislawn, E. Pruesse, Jörg Fallmann, Jerome Kelleher, Hai Nguyen, Lance L. Parsons, Zhuo-Qing Fang, E. B. Stovner, Nicholas Stoler, S. Ye, I. Wohlers, Rick Farouni, M. Freeberg, James E. Johnson, Marcel Bargull, P. Kensche, T. Webster, J. Eppley, C. Stahl, Alexander S. Rose, Alex P. Reynolds, Liang Wang, Xavier Garnier, Simon Dirmeier, Michael Knudsen, James Taylor, Avi Srivastava, Vivek Rai, Rasmus Agren, Alexander Junge, R. Guimera, Aziz Khan, S. Schmeier, Guowei He, Luca Pinello, E. Hägglund, Alexander S. Mikheyev, J. Preussner, Nicholas R. Waters, Wei Li, Jordi Capellades, A. Chande, Yuri Pirola, S. Hiltemann, M. Bendall, Sourav Singh, W. Dunn, Alexandre Drouin, T. Di Domenico, I. de Bruijn, D. Larson, D. Chicco, Elena Grassi, Giorgio Gonnella, B. Jaivarsan, Liya Wang, F. Giacomoni, Erik L. Clarke, Daniel J. Blankenberg, Camy Tran, Rob Patro, S. Laurent, Matthew Gopez, B. Sennblad, J. Baaijens, Philip A. Ewels, Patrick R. Wright, Oana M. Enache, Pierrick Roger, W. Dampier, David Koppstein, Upendra Kumar Devisetty, T. Rausch, M. Cornwell, A. Salatino, Julien Seiler, Matthieu Jung, E. Kornobis, Fabio Cumbo, David Lähnemann, Bianca K. Stöcker, O. Moskalenko, D. Bogema, M. Workentine, S. Newhouse, Felipe da Veiga Leprevost, Kevin J. Arvai, Johannes Köster · 发表于：Nature Methods · 年份：2018 · DOI：10.1038/s41592-018-0046-7 · 被引用次数：1460 · 研究领域：Medicine、Computer Science

We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform 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.