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, 2017 and 2018 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. It has turned out that it can be an extra challenge to debug and fix programs where the previously written tests have failed.
Confirmed Mentor: Andreas Tille
How to contact the mentor: firstname.lastname@example.org
Confirmed co-mentors: email@example.com
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 909706, 909707, 909708, 909709, 909710, 909711, 909713, 909715, 909716 or 909717 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