can't get bam2cfg.pl to work

[godzilla07]

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.

[GenoMax]

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.

[godzilla07]

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?

[godzilla07]

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?

[GenoMax]

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

[godzilla07]

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

[GenoMax]

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.