[BioRuby] Bio::Fetch issue - biofetch.rb not found

[Naohisa GOTO]

Hello Marc,

Sorry for late response.

> http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at 
> that location?

The service is down for years, due to the server trouble,
and it is currently difficult to restore the service
because of the internal structure of bioruby.org.

Please use other server, e.g.
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch

 bf =Bio::Fetch.new('http://www.ebi.ac.uk/Tools/dbfetch/dbfetch')
 str = bf.fetch('embl', 'AE014292')
 print str

Alternatively, some other classes provide similar function.

 str = Bio::TogoWS::REST.entry('genbank', 'AF237819')
 print str

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 19 Sep 2011 10:57:14 +0200
"Marc P. Hoeppner" <mphoeppner at gmail.com> wrote:

> Hi,
> 
> when trying to fetch entries from remote databases via Bio::Fetch, I 
> receive the following error:
> 
> /usr/lib/ruby/1.8/open-uri.rb:277:in `open_http': 404 Not Found 
> (OpenURI::HTTPError)
> 
> It appears the default entry for Fetch.new searches for 
> http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at 
> that location?
> 
> Am I doing anything wrong?
> 
> Using gem version 1.4.2 and ruby 1.8.7 on Ubuntu 11.04
> 
> /Marc
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