[BioRuby] Rake

Michael Barton mail at michaelbarton.me.uk
Thu Jan 20 20:57:26 UTC 2011

Yannick, you make an excellent point about the long term stability for boson.
The ruby community, myself often guilty of this, is quick to jump on a new gem,
which may or may not last into the future. A example of this is the Less gem
for compiling CSS which has seen some recet popularity. I believe the developer
has said he will no longer maintain it.

Another option could be Thor. I believe this is also aimed at being a more
modular rake-like tool. This is developed by Yehuda Katz and I think is used
for the basis of few mainstream ruby command line tools (possibly the rails3
CLI? I'm not 100% about this.). I think you could expect Thor to be more mature
and likely to be continually developed. If can find the episode of the
ChangeLog with Yehuda you can hear him discuss it.

On Thu, Jan 20, 2011 at 11:08:55AM +0700, Yannick Wurm wrote:
> Hello & thanks for the comments.
> Matt wrote: 
> > Swappable/configurable steps might be
> > 
> > Pre-process (trim / quality filters?) Alignment   (align) Post alignment
> > (gblocks) Translation   (to Nexus) Analysis      (Phyml)
> > 
> > The idea is that we could swap in components (TNT or RaXML for Phyml,
> > Muscle for MAFFT etc.)- but also that the pipeline remains "simple".
> Yes, thats what I would ideally want. (as well as being able to easily modify
> the run options of the programs). How would you go about generalizing this?
> Right now I'm basing "what do to" on the file extensions I provide... which
> limits me based on the file extensions...
> Michael wrote:
> > I think it's a great idea to generate predefined pipelines for common
> > bioinformatics tasks. I experimented with a tool called Boson six months
> > ago.  It could be worth looking if you feel like investing more time into
> > your pipeline.
> > 
> > Boson commands, similar to rake tasks, are more modular and can be
> > installed from the web into a ~/.boson directory. This has obvious
> > advantages over a single rake file. Boson tasks can be chained together
> > where the data is passed around in YAML format.
> > 
> > The github link is - https://github.com/cldwalker/boson
> I haven't looked thoroughly now, but at least superficially, Boson looks real
> cool.
> However, I'm a bit scared of investing energy into technologies that are too
> new. Boson has only one developer who may or may not keep his project alive
> over the next years. Time I invest in learning something today ... must
> continue to help improve my productivity over the next 5 or 10 years by still
> being reusable in 5 or 10 years (with as few modifications as possible).
> There is uncertainty to everything, but something like Boson does seems a bit
> too risky right now...
> Cheers,
> yannick
> ------------------------- Ant Genomes & Evolution http://yannick.poulet.org
> skype://yannickwurm
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