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

Grüning, Björn; Dale, Ryan; Sjödin, Andreas; Chapman, Brad; Rowe, Jillian; Tomkins-Tinch, Christopher; Valieris, Renan; Caprez, Adam; Batut, Bérénice and Haudgaard, Mathias, et al. (2017)
Abstract
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.
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keywords
Bioinformatics, Bioinformatics tools, Computational biology, Software distribution
pages
13 pages
publisher
bioRxiv
DOI
10.1101/207092
language
English
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yes
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e16b775c-3b20-4d7f-ba14-dbb85abaa8c7
date added to LUP
2017-10-31 09:59:08
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2017-10-31 15:38:21
@misc{e16b775c-3b20-4d7f-ba14-dbb85abaa8c7,
  abstract     = {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.},
  author       = {Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad and Rowe, Jillian and Tomkins-Tinch, Christopher and Valieris, Renan and Caprez, Adam and Batut, Bérénice and Haudgaard, Mathias and Cokelaer, Thomas and Beauchamp, Kyle and Pedersen, Brent and Hoogstrate, Youri and Bretaudeau, Anthony and Ryan, Devon and Le Corguillé, Gildas and Yusuf, Dilmurat and Luna-Valero, Sebastian and Kirchner, Rory and Brinda, Karel and Wollmann, Thomas and Raden, Martin and van Heeringen, Simon and Soranzo, Nicola and Pantano, Lorena and Charlop-Powers, Zachary and Unneberg, Per and De Smet, Matthias and Martin, Marcel and Von Kuster, Greg and Antao, Tiago and Miladi, Milad and Thornton, Kevin and Brueffer, Christian and van der Beek, Marius and Maticzka, Daniel and Blank, Clemens and Will, Sebastian and Gravouil, Kévin and Wolff, Joachim and Holtgrewe, Manuel and Fallmann, Jörg and Piro, Vitor and Shlyakhter, Ilya and Yousif, Ayman and Mabon, Philip and Zhang, Xiao-Ou and Shen, Wei and Cabral, Jennifer and Thomas, Cristel and Enns, Eric and Brown, Joseph and Boekel, Jorrit and de Hollander, Mattias and Kelleher, Jerome and Turaga, Nitesh and de Ruiter, Julian and Bouvier, Dave and Gladman, Simon and Choudhary, Saket and Harding, Nicholas and Eggenhofer, Florian and Kratz, Arne and Fang, Zhuoqing and Kleinkauf, Robert and Timm, Henning and Cock, Peter and Seiler, Enrico and Brislawn, Colin and Nguyen, Hai and Bakken Stovner, Endre and Ewels, Philip and Chambers, Matt and Johnson, James and Hägglund, Emil and Ye, Simon and Valls Guimera, Roman and Pruesse, Elmar and Dunn, Augustine and Parsons, Lance and Patro, Rob and Koppstein, David and Grassi, Elena and Wohlers, Inken and Reynolds, Alex and Cornwell, MacIntosh and Stoler, Nicholas and Blankenberg, Daniel and He, Guowei and Bargull, Marcel and Junge, Alexander and Farouni, Rick and Freeberg, Mallory and Singh, Sourav and Bogema, Daniel and Cumbo, Fabio and Wang, Liang-Bo and Larson, David and Workentine, Matthew and Kumar Devisetty, Upendra and Laurent, Sacha and Roger, Pierrick and Garnier, Xavier and Agren, Rasmus and Khan, Aziz and Eppley, John and Li, Wei and Stöcker, Bianca Katharina and Rausch, Tobias and Taylor, James and Wright, Patrick and Taranto, Adam and Chicco, Davide and Sennblad, Bengt and Baaijens, Jasmijn and Gopez, Matthew and Abdennur, Nezar and Milne, Iain and Preussner, Jens and Pinello, Luca and Srivastava, Avi and Chande, Aroon and Kensche, Philip Reiner and Pirola, Yuri and Knudsen, Michael and de Bruijn, Ino and Blin, Kai and Gonnella, Giorgio and Enache, Oana and Rai, Vivek and Waters, Nicholas and Hiltemann, Saskia and Bendall, Matthew and Stahl, Christoph and Miles, Alistair and Boursin, Yannick and Perez-Riverol, Yasset and Schmeier, Sebastian and Clarke, Erik and Arvai, Kevin and Jung, Matthieu and Di Domenico, Tomás and Seiler, Julien and Rasche, Eric and Kornobis, Etienne and Beisser, Daniela and Rahmann, Sven and Mikheyev, Alexander and Tran, Camy and Capellades, Jordi and Schröder, Christopher and Salatino, Adrian Emanuel and Dirmeier, Simon and Webster, Timothy and Moskalenko, Oleksandr and Stephen, Gordon and Köster, Johannes},
  keyword      = {Bioinformatics,Bioinformatics tools,Computational biology,Software distribution},
  language     = {eng},
  month        = {10},
  pages        = {13},
  publisher    = {bioRxiv},
  title        = {Bioconda: A sustainable and comprehensive software distribution for the life sciences},
  url          = {http://dx.doi.org/10.1101/207092},
  year         = {2017},
}