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

Björn Grüning,Ryan Dale,Andreas Sjödin,Brad A. 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, Sebastian Luna-Valero,Rory Kirchner, Karel Brinda,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 Antao,Milad Miladi,Kevin Thornton,Christian Brueffer,Marius van den Beek, Daniel Maticzka,Clemens Blank, Sebastian Will, K´evin Gravouil,Joachim Wolff,Manuel Holtgrewe,Jörg Fallmann,Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif,Philip Mabon, Xiao-Ou Zhang,Wei Shen,Jennifer Cabral, Cristel 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 J. A. Cock,Enrico Seiler,Colin Brislawn, Hai Nguyen,Endre Bakken Stovner,Philip Ewels, Matt Chambers, James E. Johnson,Emil Hägglund,Simon Ye, Roman Valls Guimera, Elmar Pruesse,W. Augustine 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 Agren, Aziz Khan,John M Eppley, Wei Li, Bianca Katharina Stöcker, Tobias Rausch,James Taylor,Patrick R. Wright, Adam P. Taranto,Davide Chicco,Bengt Sennblad, Jasmijn A. Baaijens,Matthew Gopez,Nezar Abdennur,Iain Milne,Jens Preussner,Luca Pinello,Avi Srivastava, Aroon T. Chande, Philip Reiner 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 Perez-Riverol,Sebastian Schmeier, Erik Clarke, Kevin Arvai, Matthieu Jung, Tom´as Di Domenico, Julien Seiler,Eric Rasche,Etienne Kornobis,Daniela Beisser,Sven Rahmann, Alexander S Mikheyev, Camy Tran, Jordi Capellades,Christopher Schröder, Adrian Emanuel Salatino,Simon Dirmeier, Timothy H. Webster,Oleksandr Moskalenko,Gordon Stephen,Johannes Köster

Nature Methods（2017）

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摘要

We present Bioconda (), 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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