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  • can't get bam2cfg.pl to work

    I am using breakdancer1.1.2 and I've downloaded the two CPAN files for the bam2cfg.pl program but when I run the program bam2cfg.pl on 3 bam files I get:
    Can't locate Statistics/Descriptive.pm in @INC (@INC contains /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bam2cfg.pl line 7.
    BEGIN failed--compilation aborted at bam2cfg.pl line 7.

    Any suggestions are appreciated.

  • #2
    Looks like you need to install this module: http://search.cpan.org/~shlomif/Stat...Descriptive.pm If it is installed then it is not in the @INC path. You can add that to path by http://www.perlhowto.com/extending_the_library_path.

    Comment


    • #3
      Thankyou for your suggestion. I put the 2 modules into the @INC path but it still can't find the modules in @INC when I use bam2cfg. I also tried to modify the script by putting use lib "path to module" at the beginning of the bam2cfg script but I still keep getting the same error message! This is very frustrating.
      Is there a proper way to install these CPAN modules?

      Comment


      • #4
        I was finally able to install the 2 modules Statistics:escriptive and Math::CDF modules correctly as root but now the bam2cfg program stops at line8 which is use GD::Graph::histogram. This module is not mentioned in the web page http://breakdancer.sourceforge.net/moreperl.html I tried to install this module using cpan but all of the make_tests are NO. How can I install this module correctly?

        Comment


        • #5
          Originally posted by godzilla07 View Post
          I was finally able to install the 2 modules Statistics:escriptive and Math::CDF modules correctly as root but now the bam2cfg program stops at line8 which is use GD::Graph::histogram. This module is not mentioned in the web page http://breakdancer.sourceforge.net/moreperl.html I tried to install this module using cpan but all of the make_tests are NO. How can I install this module correctly?
          See if this helps: http://www.walkingrandomly.com/?p=55

          Comment


          • #6
            breakdancer1.1.2 problems

            Thankyou GenoMax. I got bam2cfg.pl to finally work but now I can't get BreakDancerMax.cpp to work. When I use the command
            perl BreakDancerMax.cpp -t -q 10 -d config.ctx config.cfg > config.ctx, I get the below message. I had downloaded Breakdancer1.1.2 and this version does not have breakdancermax.pl. I don't know if this is the right command since I do not know what a .cpp file is.

            (Missing operator before main?)
            Operator or semicolon missing before *argv at BreakDancerMax.cpp line 11.
            Ambiguous use of * resolved as operator * at BreakDancerMax.cpp line 11.
            Bareword found where operator expected at BreakDancerMax.cpp line 14, near "// chromosome"
            (Missing operator before chromosome?)
            Bareword found where operator expected at BreakDancerMax.cpp line 20, near "//temporarily"
            (Missing operator before temporarily?)
            Bareword found where operator expected at BreakDancerMax.cpp line 21, near "//bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 23, near "//bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 24, near "//bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 25, near "// bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 26, near "// bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 28, near "//bool"
            (Missing operator before bool?)
            Bareword found where operator expected at BreakDancerMax.cpp line 29, near "//bool"
            (Missing operator before bool?)
            syntax error at BreakDancerMax.cpp line 11, near "// main function
            "
            syntax error at BreakDancerMax.cpp line 15, near "// chromosome
            "
            syntax error at BreakDancerMax.cpp line 20, near "//temporarily "
            syntax error at BreakDancerMax.cpp line 22, near "//bool
            float "
            syntax error at BreakDancerMax.cpp line 24, near "//bool
            "
            syntax error at BreakDancerMax.cpp line 25, near "//bool
            "
            syntax error at BreakDancerMax.cpp line 26, near "// bool
            "
            syntax error at BreakDancerMax.cpp line 27, near "// bool
            "
            syntax error at BreakDancerMax.cpp line 29, near "//bool
            "
            syntax error at BreakDancerMax.cpp line 30, near "//bool
            "
            BreakDancerMax.cpp has too many errors.

            Any help is appreciated. Thankyou

            Comment


            • #7
              There are two versions of breakdancer. The one you are referencing now (*.cpp) is a C program file. This will not work with perl.

              Perl version: http://breakdancer.sourceforge.net/moreperl.html
              C version: http://breakdancer.sourceforge.net/morecpp.html See the section on differences from Perl version.

              Comment

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