You wrote it, Now Get it used: Publishing your software with galaxy and bioconda

Daniel Blankenberg, Martin Čech

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

You’ve written software, published the code, and described it in a paper. Now, how do you make your software stand out and actually get used? This tutorial introduces two technologies that can make it easy to deploy by researchers around the world and greatly increase your software’s reach. Bioconda (https://bioconda.github.io/) is a platform for packaging and publishing bioinformatics software using Conda (http://conda.pydata.org/docs/intro.html). The Conda package manager does what previous language and platform specific packagers (e.g., pip, CPAN, CRAN, Bioconductor, apt-get) have done, but in a language and OS agnostic, and much more streamlined way. Tools in Bioconda are easy for infrastructure providers and other researchers to deploy and use. We will introduce Conda and Bioconda principles, and then guide participants through packaging a tool with Bioconda. Participants will package their newly created Bioconda tool for Galaxy (https://galaxyproject.org/), a widely deployed platform for data integration and analysis in life science research. We will define and test the Bioconda-encapsulated tool for Galaxy and then publish it in the Galaxy Toolshed, where any Galaxy administrator can then install it with a button click. This will be hands-on. Please bring a wifi-enabled laptop. Instructors will work with participants to install needed software before the conference.

Original languageEnglish (US)
Title of host publicationACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
PublisherAssociation for Computing Machinery, Inc
Number of pages1
ISBN (Electronic)9781450366663
DOIs
StatePublished - Sep 4 2019
Event10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2019 - Niagara Falls, United States
Duration: Sep 7 2019Sep 10 2019

Publication series

NameACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Conference

Conference10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2019
CountryUnited States
CityNiagara Falls
Period9/7/199/10/19

Fingerprint

Galaxies
Software
Product Packaging
Packaging
Language
Research Personnel
Data integration
Bioinformatics
Biological Science Disciplines
Computational Biology
Administrative Personnel
Managers
Technology
Research

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Software
  • Biomedical Engineering
  • Health Informatics

Cite this

Blankenberg, D., & Čech, M. (2019). You wrote it, Now Get it used: Publishing your software with galaxy and bioconda. In ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics). Association for Computing Machinery, Inc. https://doi.org/10.1145/3307339.3343178
Blankenberg, Daniel ; Čech, Martin. / You wrote it, Now Get it used : Publishing your software with galaxy and bioconda. ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Association for Computing Machinery, Inc, 2019. (ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics).
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abstract = "You’ve written software, published the code, and described it in a paper. Now, how do you make your software stand out and actually get used? This tutorial introduces two technologies that can make it easy to deploy by researchers around the world and greatly increase your software’s reach. Bioconda (https://bioconda.github.io/) is a platform for packaging and publishing bioinformatics software using Conda (http://conda.pydata.org/docs/intro.html). The Conda package manager does what previous language and platform specific packagers (e.g., pip, CPAN, CRAN, Bioconductor, apt-get) have done, but in a language and OS agnostic, and much more streamlined way. Tools in Bioconda are easy for infrastructure providers and other researchers to deploy and use. We will introduce Conda and Bioconda principles, and then guide participants through packaging a tool with Bioconda. Participants will package their newly created Bioconda tool for Galaxy (https://galaxyproject.org/), a widely deployed platform for data integration and analysis in life science research. We will define and test the Bioconda-encapsulated tool for Galaxy and then publish it in the Galaxy Toolshed, where any Galaxy administrator can then install it with a button click. This will be hands-on. Please bring a wifi-enabled laptop. Instructors will work with participants to install needed software before the conference.",
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Blankenberg, D & Čech, M 2019, You wrote it, Now Get it used: Publishing your software with galaxy and bioconda. in ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Association for Computing Machinery, Inc, 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2019, Niagara Falls, United States, 9/7/19. https://doi.org/10.1145/3307339.3343178

You wrote it, Now Get it used : Publishing your software with galaxy and bioconda. / Blankenberg, Daniel; Čech, Martin.

ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Association for Computing Machinery, Inc, 2019. (ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Blankenberg D, Čech M. You wrote it, Now Get it used: Publishing your software with galaxy and bioconda. In ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Association for Computing Machinery, Inc. 2019. (ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics). https://doi.org/10.1145/3307339.3343178