You wrote it, now get it used: Publishing your software with Galaxy and Bioconda
Software reuse, made easy
- Date: September 7th 2019- September 10th 2019
- Location: ACM BCB, Niagara Falls, New York, United States
- Contact: Dan Blankenberg, Martin Čech
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 is a platform for packaging and publishing bioinformatics software using Conda. 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, 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.
Prerequisites for this tutorial
- Have a wifi-enabled laptop for the hands-on parts of the tutorial.
- Have a basic familiarity with the Unix/Linux shell
The tutorial will be held the first day of the conference, Saturday, September 7.