15 May 2014

How I start a bioinformatics project

Phil Ashton tweeted a link to a paper about how to set up a bioinformatics project file hierarchy: " A Quick Guide to Organizing Computational Biology Projects ".

Nick Loman posted his version yesterday : "How I start a bioinformatics project" on http://nickloman.github.io/2014/05/14/how-i-start-a-bioinformatics-project/.

Here is mine (simplified):

  • I start by creating a directory managed by git
  • I create a JSON-based description of my data, including the path to the softwares, to the references
  • I create a git submodule for a project hosting an Apache-velocity template transforming a Makefile from config.json :
  • The Makefile is generated using jsvelocity :It produces the following Makefile:
  • The Makefile is invoked with option -j N(Allow N jobs at once) using GNU-Make or QMake(distributed parallel make, scheduled by Sun Grid Engine)

That's it,


No comments: