I took a look at your site, downloaded the source and went through both tutorials. The first 5 minute tutorial took me much more than 5 minutes, the second took me much less! Anyway, I think that this is the Susan Boyle of bioinformatics- I didn't expect much out of it because it was not pretty. I am familiar with the graphic-based pipeline builders like VIBE and Pipeline Pilot, and these are much prettier. Still, I think that what you have created is very valuable for at least a couple of reasons.
First, many programmers do not want to use visual 'drag and drop' type tools. These tools are aimed more at non-programmers, but in my experience biologists would rather hire someone to create a pipeline anyway. Second, your module is free and most of the other tools are not. While something like Pipeline Pilot is a wonderful system in the long run, most people just want to get something done today, and don't want to spend money to do it. Third, if I am creating a pipeline in Python, then your module simply makes things easier and more efficient. To switch to another system is an extra learning step that I don't need. Again, people generally want to solve the problem at hand, not to create another issue. Fourth, I like the error-checking and restart capabilities because I have had trouble with that in the past! Best regards, Martin Gollery ---------- Forwarded message ---------- From: Leo Goodstadt <[email protected]> Date: Mon, Jun 1, 2009 at 7:01 AM Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics To: [email protected] 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 -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
