[Biococoa-dev] BioCocoa linux install

Scott Christley schristley at mac.com
Thu Mar 27 15:29:40 EDT 2008


Hello Paolo,


On Mar 27, 2008, at 1:08 PM, paolo siniselli wrote:

> debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/ 
> obj#
> . /usr/share/GNUstep/Makefiles/GNUstep.sh

Correct, sourcing that script sets up the GNUstep environment.  If  
you do not want to type it each time you open a terminal window, you  
can add it to your .bashrc or .bash_profile script in your home  
directory.


>
> .:3: validity error : Validation failed: no DTD found
> !
> <plist version="0.9">
>                     ^
> .:3: validity error : Validation failed: no DTD found
> !
> <plist version="0.9">
>                     ^
> .:3: validity error : Validation failed: no DTD found
> !
> <plist version="0.9">
>                     ^


These messages do not look good.  Seems to indicate that something is  
wrong with the XML parsing in GNUstep.  It is necessary for the XML  
parsing to be enabled and functional with GNUstep in order for  
BioCocoa to work.



>
> I don't know what those errors mean, and I don't know
> know about the parameter f and r which ared used in
> construct_sarray.

The f/r parameter is to specify just the forward or reverse strand to  
be used.  It is an optional parameter and normally do not specify so  
that both strands are used.

cheers
Scott





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