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And running 'make' again.
Note: It is now assumed that you are in the breakdancer directory, inside it you've placed a samtools-0.1.6 directory and have compiled the samtools directory.
Alter Breakdancer's Makefile
...
Congrats! You've, hopefully, installed the CPP portion of Breakdancer. But there is also a Perl script that Breakdancer must run so we need to handle the prerequisites for that.
Prerequisites for bam2cfg.pl
Change the shebang/header in the bam2cfp.pl from:
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#!/gsc/bin/perl
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to
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#!/usr/bin/env perl
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Install the required perl modules.
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sudo cpan install Math::CDF
sudo cpan install Statistics::Descriptive
sudo cpan install GD::Graph
sudo cpan install GD::Graph::histogram
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Running Breakdancer
For sanity just update you PATH environmental variable to include looking into the breakdancer directory for bam2cfg.pl and breakdancer_max.