[Bioc-devel] sequencing workflow

Dan Tenenbaum dtenenba at fhcrc.org
Wed Dec 18 01:31:57 CET 2013

Hi Michael,

----- Original Message -----
> From: "Michael Lawrence" <lawrence.michael at gene.com>
> To: bioc-devel at r-project.org
> Sent: Tuesday, December 17, 2013 4:26:20 PM
> Subject: [Bioc-devel] sequencing workflow
> Hey guys,
> I was just checking out the workflows on the Bioc website, putting
> myself
> in the mindset of a naive user. At first glance, the sequencing
> workflow is
> pretty intimidating. There's a lot of code and text in a _tiny_ font,
> the
> examples do not run out of the box, and they expect the user to
> create a
> particular directory layout just to get started.

Thanks for the comments. The sequencing workflow is fairly old and it is the only one of our workflows that is not actually evaluated regularly by R (see the About This Document section of the other workflows). 

It is certainly due for an overhaul. Whoever does that, get in touch with me and I'll let you know how the workflow builder works.


> What about starting with a cookbook-style tour of the neat things one
> can
> do with ranges and sequences, and then integrate everything into a
> complete
> workflow at the end? With sample data made immediately available. For
> example, while running a ShortRead QA report is the right thing to do
> when
> starting from a FASTQ, it might not be the best thing for selling the
> user
> on the richness of the environment, and the coolness of how the tools
> interoperate. Just some thoughts. Not volunteering ;)
> An important thing to keep in mind is that if the user tries to run
> the
> examples on a full-scale dataset, they are only going to succeed in
> crashing their machine. So either we need to teach them how to write
> scalable code, or we need to provide high-level functionality that
> handles
> that for them, until they are ready to dig deeper.
> Michael
> 	[[alternative HTML version deleted]]
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