This page was last updated on Friday, 11-Nov-2016 11:44:32 CST

Installation notes for BreakDancer version 1.1

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Prerequisites

• svn
  $ sudo apt-get install subversion
• Perl modules
  • Statistics::Descriptive
  • Math::CDF
  • GD::Graph::histogram
  $ sudo cpan Statistics::Descriptive Math::CDF GD::Graph::histogram
• Samtools development version. See samtools install notes.
  Header files are located in /usr/lib/samtools/

Installation

1. $ cd /programinstallers/
2. $ svn checkout https://github.com/kenchen/breakdancer
   ...
   Checked out revision 24.
3. $ cd /programinstallers/breakdancer/trunk/cpp
4. Change Makefile from

   all:
   	g++ -g -Wall -O2 -I/gsc/pkg/bio/samtools/samtools-0.1.6/ BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer_max -lm -lz -L/gsc/pkg/bio/samtools/samtools-0.1.6/ -lbam

   To

   all:
   	g++ -g -Wall -O2 -I/usr/lib/samtools/ BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer_max -lm -lz -L/usr/lib/samtools/ -lbam -pthread -lz

5. $ make
6. $ cd /programinstallers/breakdancer/trunk/perl
7. Edit Perl path
   $ nano bam2cfg.pl
   Change first line from
   #!/gsc/bin/perl
   To
   #!/usr/bin/perl
8. These are the older version 1.0 programs:
   $ cd /programinstallers/breakdancer/branches/release-r76
9. Fix the Perl paths as above for the two files BreakDancerMax.pl and BreakDancerMini.pl
10. For these files, also set a location for breakdancer modules Poisson.pm or AlnParser.pm, e.g. Local::Poisson.pm
11. $ cd /programinstallers
12. Installation
    $ cp -puv breakdancer/trunk/cpp/breakdancer_max breakdancer/trunk/perl/bam2cfg.pl breakdancer/branches/release-r76/BreakDancerM*.pl /usr/local/bin/
    

    `breakdancer/trunk/cpp/breakdancer_max' -> `/usr/local/bin/breakdancer_max'
    `breakdancer/trunk/perl/bam2cfg.pl' -> `/usr/local/bin/bam2cfg.pl'
    `breakdancer/branches/release-r76/BreakDancerMax.pl' -> `/usr/local/bin/BreakDancerMax.pl'
    `breakdancer/branches/release-r76/BreakDancerMini.pl' -> `/usr/local/bin/BreakDancerMini.pl'

13. $ cp -puv breakdancer/trunk/perl/*.pm /usr/share/perl5/Local/
    

    `breakdancer/trunk/perl/AlnParser.pm' -> `/usr/share/perl5/Local/AlnParser.pm'
    `breakdancer/trunk/perl/Poisson.pm' -> `/usr/share/perl5/Local/Poisson.pm'

14. For documentation web page:
    $ mkdir web/breakdancer
15. $ cp -puv breakdancer/trunk/README web/breakdancer/README.txt
16. Cleanup
    $ cd /programinstallers ; rm breakdancer -rf