[BioRuby] Using CPAN

[Toshiaki Katayama]

Hi,

On 2004/01/08, at 17:06, pjotr at pckassa.com wrote:
> Great! We are back on-line.

I'm gradually correcting web pages, wiki documents and will start to
commit recent changes into cvs.

> I have a generic idea to write a module which would allow using CPAN
> from Ruby:

The idea is interesting, however, it seems that slightly off topic for
this list as it is not limited to the *bio* ruby.


Anyway, I have some comments, ;)

> The idea is to fire up a Perl XML/RPC or SOAP server from Ruby and use 
> a
> simple interface for calling Perl.

I became to like SOAP before trying XMLRPC as it was easy to use,
usually needless to care about the data type especially in Ruby
as SOAP4R automatically converts into Ruby's object.

I use SOAP for the KEGG API (http://www.genome.ad.jp/kegg/soap/).

> The reason I am writing this to the list is if to see if there are
> other parties interested.

I think you should try the ruby-talk list for this purpose.
Have you see http://www.yoshidam.net/Ruby.html#perl already?

> Ruby RAA is quite good, but I am envious
> about some of the BioPerl facilities and modules like Mail::Box. I
> could help people choosing Ruby since it has BioPerl support(!). What
> do you think?

I can understand your point and BioPerl is really great, however,
we shold try to implement the needed functionality in rubyish style.

To use Perl from Ruby requires a knowledge of Perl.  I feel that
writing Perl script is easier than eval("$perl_code") in this case.

As for the Mail::Box, I don't know what you really want to do with it,
however, mailread.rb coming with Ruby(!) is enough for printing out
headers and there are many other libraries for mail, smtp, pop and
imap already.

Finally, back to the BioRuby, Ruby 1.6.8 + RAA:ruby-sumo or recently
released Ruby 1.8.1 will give us an enough environment to start with.
See
   http://bioruby.org/wiki/English/?How+do+I+get+and+install+BioRuby%3F
in the 'BioRuby in Anger' document for more details.

Thanks,
Toshiaki Katayama