Continuous Integration for biological applications inside Debian
Description of the project: The Debian Med project has packaged a lot of applications for bioinformatics. In 2016 and 2017 Outreachy students did a great job in adding autopkgtests to several packages. This is considered a big step for Continuous Integration for applications in bioinformatics. Due to the great success and the very positive response of the students a continuation of this effort to cover even more applications with sensible test suites should be done.
Confirmed Mentor: Andreas Tille
How to contact the mentor: tille@debian.org
Confirmed co-mentors:
Deliverables of the project: Enhanced packages for bioinformatics covering whole workflows of users as best as possible
Desirable skills: The student should have a background in bioinformatics. Debian packaging skills are an extra plus but can be taught in the project run.
What the intern will learn: Detailed insight into the bioinformatic tools inside Debian, Comparing and benchmarking biotools, Debian packaging skills, Optimising bioinformatics and other scientific tools
Application tasks: Pick one of these bugs 879616, 879617, 879618, 879621, 879622 and try fixing it - asking the mentor for help is fine. This is on one hand proof that the students is able to understand Debian packaging and understands bioinformatics at a sufficient level
Related projects: SummerOfCode2016/Projects/BioToolsTesting, SummerOfCode2017/Projects/QA_BiologyApps