official examples could not run --- bioinformatics toolbox

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);

[Walter Roberson]

Which Linux are you using?

[Shuoguo]

redhat enterprise server, version 6.3

genome 2.282

thanks

Answer 1

[Lucio Cetto]

This a known issue. There are workarounds already published.

http://www.mathworks.com/support/bugreports/865214

HTH

Lucio

[Shuoguo]

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

Answer 2

[Jason Ross]

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.