[BioRuby] Using CPAN

[pjotr at pckassa.com]

On Sun, Jan 11, 2004 at 06:56:31AM +0900, Toshiaki Katayama wrote:
> The idea is interesting, however, it seems that slightly off topic for
> this list as it is not limited to the *bio* ruby.

No, it is generic. But then it also applies to some facilities of CPAN
which may not be in BioRuby, but still useful for biologists.

> 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/).

I have used both. SOAP is very good too, and in fact more complete
than XMLRPC. The only disadvantage is slightly higher
overhead/complexity. I was planning a factory pattern for the
transport mechanism. So SOAP can be plugged in.

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

I checked that. The problem is you have to actively link Perl against
Ruby - which complicates matters (certainly during deployment). I like
the idea of fixing things at runtime.

I just wonder why no one else has come up with my idea. Performance
reasons? Or just because we believe we have to duplicate everything?
Only one way to find out...

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

We should - and will. I will also try to contribute. But in life
sometimes one has to take short cuts. If there is something that
immediately works...

But like I wrote earlier - it may be just theory - we may attract
bio-informaticians if they believe they can use CPAN with Ruby. I
think we need to expand our community.

Note: the installation procedure of CPAN really shines (resolving
dependencies, testing, documentation etc.). I tried raa-install, but
that did not give good feelings. You see, CPAN is more than just code.
Ruby is still weak in that area.

> 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.

Yes and no. The thing is to use a lot of Ruby and just the Perl for
the libraries.

Anyway, thanks for your comments. I am testing the water so to speak.
Lets see if I can get something written in the coming period. If
anyone is interested please drop me a mail.

Pj.