official examples could not run --- bioinformatics toolbox

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Shuoguo
Shuoguo am 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);
  2 Kommentare
Walter Roberson
Walter Roberson am 27 Sep. 2012
Which Linux are you using?
Shuoguo
Shuoguo am 28 Sep. 2012
redhat enterprise server, version 6.3
genome 2.282
thanks

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Akzeptierte Antwort

Lucio Cetto
Lucio Cetto am 28 Sep. 2012
This a known issue. There are workarounds already published.
HTH
Lucio
  1 Kommentar
Shuoguo
Shuoguo am 28 Sep. 2012
Bearbeitet: Shuoguo am 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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Weitere Antworten (1)

Jason Ross
Jason Ross am 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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