Makefile Lab Meeting
Makefile lab meeting
12 noon, Wednesday 4/4, 2007, 425 Hearst Mining Building (see Lab Meetings)
The topic of this meeting was the use of automated build tools for bioinformatics pipelines. (See, for example, this intro on nodalpoint.org, or Parker et al.: Evolving from bioinformatics in-the-small to bioinformatics in-the-large. OMICS 2003;7:37-48..)
The conclusions of the meeting are summarized on the Make Comparison page.
George recommended Rose-DB as a Perl database interface.
Proposed assignments in parentheses.
- Why make?
- Parker et al.: Evolving from bioinformatics in-the-small to bioinformatics in-the-large. OMICS 2003;7:37-48. by Lee et al (PDF) (Ian)
- Make use cases: Rfam analyses, fly zipcodes, fly RNA scan... (Ian)
- How make should work: Bio Make and Skam (Ian, with backup from Chris)
- What's wrong with GNU make: Makefile Manifesto (Andrew)
- Parallel processing
- Roll-your-own make replacements
A few practical issues to think about:
- What's real (i.e. implemented)?
- What's re-useable?
- What fancy systems could be real, with a little work?
- What could you do with those fancy systems that you couldn't do before?
-- Made Guys - 21 Mar 2007