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Reproducible bioinformatics pipelines using Make
- dalke 11y agoChris Mungall did a presentation in 2004 on "BioMake: Functional Logical Task Management for Bioinformatics" http://open-bio.org/bosc2004/accepted_abstracts.html#mungall http://open-bio.org/bosc2004/accepted_abstracts.html#mungall : > For our in-house task management we required something similar to Makefiles in terms of level of abstraction and simplicity, yet without the limitations of Makefiles and related systems (ant, scons, build, etc). In particular we needed: - Asynchrnonous task management on compute farms - Choice of either relational database or filesystem for storing build targets - A cleaner specification language - Fully programmable logic within the Makefile specification That's about the time I stopped following bioinformatics, and I don't know what happened with it. (It's also the same conference where I discovered some whiskeys I liked. Coincidence?)