official examples could not run --- bioinformatics toolbox

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Shuoguo
Shuoguo on 27 Sep 2012
r = {'ACGACTGC', 'ACGTTGC', 'AGGTATC'}; % unaligned sequences
c = {'3M1D1M1I3M', '4M1D1P3M', '5M1P1M1D1M'}; % cigar strings
aln1 = cigar2align(r, c)
Error using bioinfoprivate.cigar2gappedsequencemex
Invalid MEX-file
'/usr/local/MATLAB/R2012a/toolbox/bioinfo/bioinfo/+bioinfoprivate/cigar2gappedsequencemex.mexa64':
/usr/local/MATLAB/R2012a/bin/glnxa64/libbam.so.0: undefined symbol: gzopen64
Error in bioinfoprivate.cigar2gappedsequence (line 61)
[gs ap ir] = bioinfoprivate.cigar2gappedsequencemex(seqs,cigars,SoftClipping,GapsInRef,Quality);
Error in cigar2align (line 72)
[gs,ap,ri] =
bioinfoprivate.cigar2gappedsequence(seqs,cigars,'GapsInRef',doGapsInRef,'softClipping',includeSoftClipping);

Accepted Answer

Lucio Cetto
Lucio Cetto on 28 Sep 2012
This a known issue. There are workarounds already published.
HTH
Lucio
  1 Comment
Shuoguo
Shuoguo on 28 Sep 2012
Thanks! Except the last command "setenv" does not work (said not found)
used the following command and worked:
export LD_LIBRARY_PATH=$MATLAB$\toolbox\bioinfo\bioinfo\+bioinfoprivate

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More Answers (1)

Jason Ross
Jason Ross on 28 Sep 2012
A quick google search of the "undefined symbol: gzopen64" yielded a variety of responses, all which seemed to revolve around the presence and configuration of the "zlib" library. It seems that some instances of this library have "gzopen64" defined, and others do not.
There wasn't one concrete solution to getting it to work -- some people recompiled zlib, others made soft links, others found they needed to change the library paths so that it could be found, or had found multiple versions on their system.

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