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

Josh Cherry jcherry at ncbi.nlm.nih.gov
Thu Aug 7 14:04:17 EDT 2008


Support for other OS's is definitely a possibility, depending on community 
feedback (how useful are the wrappers in general, and how much demand is 
there for them on other platforms?).  I wish I could magically make them 
available for Windows and OS X, but there are some technical issues to 
work out.


On Thu, 7 Aug 2008, Chris Fields wrote:

> Josh,
> 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.
> chris
> 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 
>> 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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