[Bioperl-l] NCBI C++ Toolkit wrapper (was: not BioPerl)

Chris Fields cjfields at illinois.edu
Thu Aug 7 13:38:53 EDT 2008


Thanks for the update.  I saw that these are only binaries for linux  
32/64-bit.  Are there plans to either support other OS's (OS X, Win,  
etc) or to maybe make a release with the XS-bindings so users can work  
towards that?  With additional support I can see this easily fitting  
into several spots in BioPerl, but otherwise I'm unsure.


On Aug 7, 2008, at 12:06 PM, Josh Cherry wrote:

> For those who may be wondering what this is about, a Perl interface  
> to the NCBI C++ Toolkit is available at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ 
> .  The C++ Toolkit is the main code base that we develop and use at  
> NCBI.  It includes many things that may be of interest to BioPerl  
> users, such as sequence analysis algorithms, means for interacting  
> with NCBI databases, and facilities for reading, writing, and  
> manipulating NCBI data model objects (usually defined by ASN.1  
> specifications; writeable as ASN.1, XML, and JSON, and readable from  
> ASN.1 and XML).
> Russell, I think you can make things work from behind a firewall by  
> setting some environment variables: set CONN_FIREWALL to 1, possibly  
> set CONN_STATELESS to 1, and set CONN_HTTP_PROXY_HOST and  
> CONN_HTTP_PROXY_PORT as appropriate.  Please email me if you can't  
> get things to work.  I'll see that decent instructions for this are  
> included in the next release.
> Josh Cherry
> On Aug 6, 2008, at 4:20 PM, Smithies, Russell wrote:
>> Has anyone taken a look at the new Perl interface to the NCBI C++
>> Toolkit?
>> Unfortunately, I can't even get their examples working as I'm  
>> behind a
>> firewall and documentation on setting proxy stuff is virtually
>> non-existant  :-(
>> Russell Smithies
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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