[BioRuby] Ruby installation

[Gianluca Della Vedova]

On 01/05/2014 at 08:31, Pjotr Prins wrote:

>So we are proposing that newbies use a VM, instead of building from
>source? Sorry guys, but that solution does not work for my 'newbie'
>use case. We are still offering expert advice here to experts. The
>main downside of a VM is that you need to teach someone to use a
>second environment.

I agree with you that VMs are not ok if the audience is not skilled 
enough. There is also a second problem: they usually have to leave the 
VM at the lab, so they cannot bring the new environment (and the 
customization they have accumulated) at home or work.
Will they be able to replicate everything they have practiced? I doubt 
so.

Pjotr, you are right that deployment is a problem, especially with ruby.  
The solution is not easy, and I am very interested into developing a 
suitable solution for newbies.

>
>When I give the instruction:
>
>  apt-get install ruby
>  gem install bioruby-table
>
>it should just work out of the box. Anywhere.

Yes. If it doesn't work it's a serious bug, and we should pester (and 
help) the maintainers.

>
>I am actually looking at GNU GUIX
>
>  https://news.ycombinator.com/item?id=6891214
>
>which, as it happens, works great in Docker too. The future should look
>
>  apt-get install guix
>  guix install ruby
>  gem install bioruby-table

I don't think so (TM) :-)
3 different tools to cover more-or-less the same needs are too many.
I would very much prefer a future with 1 or 2 of those tools. Do you 
think that nix/guix could easily replace gem/pip/cabal? That would be 
something that could take traction.


>which is a binary install and should work in any environment.
>
>Let's fix Ruby/Perl/Python dependency hell for once and all. It is not
>that hard with the right choices. GUIX/NIX gets things right, unlike
>rvm, VM's, and such.
>
>Pj. (lone prophet in desert)
>
>On Wed, Apr 30, 2014 at 06:27:33PM -0700, Michael Barton wrote:
>> I have been using Docker a lot. I think it's excellent. The ability to wrap
>> a program up with it's own environment is very powerful. For example you
>> can upgrade software to faster, newer runtimes without having to wait to
>> upgrade the global system runtime.
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