A new library called Ruffus is available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html.
Ruffus provides easy / lightweight support for running computational pipelines in python. The best way to produce reproducible bioinformatics analyses is by scripting all the stages or tasks which have to be run. Ruffus is designed to allow this to happen in python in the least intrusive manner possible, and without any special (non-python) syntax. Like makefiles (or scons), it helps you to manage task dependencies. However, because it is designed from the start for bioinformatics pipelines (rather than compiling programmes), no ugly syntax / hacking is required. Ruffus provides automatic support for * Managing dependencies * Running tasks in parallel * Re-starting from arbitrary points, especially after errors * Display of the pipeline as a flowchart * Reporting We have been using Ruffus in-house but we would like to see what other scientists think of the design before we bring its attention to a wider audience. (We intend to publish this as an application note in some bioinformatics journal) Please help us by sending feedback to: [email protected] Extensive documentation, download details and two tutorials are available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. Leo Goodstadt MRC Functional Genomics Unit University of Oxford _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
