TY - GEN
T1 - You wrote it, Now Get it used
T2 - 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2019
AU - Blankenberg, Daniel
AU - Čech, Martin
PY - 2019/9/4
Y1 - 2019/9/4
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85073171552&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85073171552&partnerID=8YFLogxK
U2 - 10.1145/3307339.3343178
DO - 10.1145/3307339.3343178
M3 - Conference contribution
T3 - ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
BT - ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
PB - Association for Computing Machinery, Inc
Y2 - 7 September 2019 through 10 September 2019
ER -