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  • Need help for installation of AMOS-2.0.8

    Hi friends,

    I am trying to install AMOS on my Ubuntu 9.10 system, it configure allright, but the problem is when applying "make" it gives following errors,


    IDMap_AMOS.cc: In member function ‘void AMOS::IDMap_t::read(const std::string&)’:
    IDMap_AMOS.cc:504: error: ‘fopen’ was not declared in this scope
    IDMap_AMOS.cc:509: error: ‘fscanf’ was not declared in this scope
    IDMap_AMOS.cc:515: error: ‘fscanf’ was not declared in this scope
    IDMap_AMOS.cc:517: error: ‘getc’ was not declared in this scope
    IDMap_AMOS.cc:529: error: ‘EOF’ was not declared in this scope
    IDMap_AMOS.cc:540: error: ‘EOF’ was not declared in this scope
    IDMap_AMOS.cc:557: error: ‘fclose’ was not declared in this scope
    make[3]: *** [libAMOS_a-IDMap_AMOS.o] Error 1
    make[3]: Leaving directory `/home/orf/amos-2.0.8/src/AMOS'
    make[2]: *** [all-recursive] Error 1
    make[2]: Leaving directory `/home/orf/amos-2.0.8/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/orf/amos-2.0.8'
    make: *** [all] Error 2

    Why?

    And another thing i am trying to get BAM/SAM files using *_sorted.dat/.bin as said in the manual of MOSAIK, using MosaikText but i think it is not giving right output (output file size = 0 bytes).

    When i open it in Gambit it shows nothing, it only shows name of the reference sequence, bases are not displayed.

    Is there any other tool for conversion of Mosaik result to SAM/BAM format?

  • #2
    Check this thread on how to install AMOS:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
    L. Collado Torres, Ph.D. student in Biostatistics.

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