[BioRuby] Ruby installation

[Michael Barton]

Docker is not really a VM. I think it is more a self-contained application
than can run on anyoperating system that supports it. At the moment that is
unfortunately on Linux and Mac OSX with boot2docker. I know that was not
the point you were making about using VMs though. I just write this to
highlight the difference. I agree that expecting someone to use a VM is
asking a lot.

I also agree with your point that expecting beginners to start using a VM
is a step learning curve. However I would argue that, very often, the
current state in bioinformatics is that we expect beginners to download
source code, compile it, then install half a dozen other dependencies too.
Usually after doing these steps, the software may not even work anyway.

The nice thing about something like Docker, is that if someone published
their code as a docker container then everyone would only need to learn how
to install docker containers. The underlying dependencies would be
completely masked.


On 1 May 2014 17:31, Joachim Baran <joachim.baran at gmail.com> wrote:

> Hi!
>
> On 1 May 2014 17:18, Iain Barnett <iainspeed at gmail.com> wrote:
>
> > You *provide* the VM. You *provide* the files. You *provide* the tools
> you
> > used to build the VM. You *provide* the process you used. Then anyone can
> > jump in at any level, either just load a file, or load a file and
> > reconfigure, or tweak your process and dump whatever isn't wanted.
> >
>   I think only a few bioinformaticians would actually go through that
> process -- probably many more if everything were very easy and well
> explained. I would bet that simply no single biologist or statistician
> would be willing to load their data this way.
>
> >
> > Either you want things configurable and bespoke, or you want them simple
> > and straightforward. You can't have your cake and eat it.
> >
>   That is true. I still would like to hear from others the reasons why 'gem
> install bio' fails. Are there dependencies that should be culled?
>
> Kim
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