[Biococoa-dev] BioCocoa linux install

paolo siniselli paolo_siniselli at yahoo.it
Thu Mar 27 13:08:02 EDT 2008


Ok, I did this, to solve it:

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

debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/obj#
./construct_sarray /home/kei/S_Cerevisae\
Genome/chr1.fa outputchr1 f

Constructing suffix array.
.: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">
                    ^
totSize: 1841672
maxMem: 1327878144
Sufficient memory for all sequences.
230209 bytes
Allocating 230211 bytes.
total size 230209 (bp)
Saving suffix array.

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.
Anyway, is the output file correct?
Thanks
Paolo

--- Scott Christley <schristley at mac.com> wrote:

> Your GNUstep environment is likely not setup
> properly in that  
> terminal window.  It should have added the
> appropriate paths to the  
> LD_LIBRARY_PATH environment variable so that it
> finds the shared  
> libraries


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