This page was last updated on Wednesday, 22-Jan-2014 16:11:25 CST

Installation notes for cnD version 1.3 Feb 16, 2012

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Prerequisites

None

• gdc
  1. Ubuntu was easy:
     $ sudo apt-get install gcd
  2. But not needed, cnD includes a pre-compiled binary, why don't the instructions say this?
• Tango
  1. $ sudo yum install tango-devel
• Set::IntSpan Perl module
  
  1. $ sudo cpan Set::IntSpan

Installation

1. $ cd /programinstallers/
2. $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/cnd/cnD-1.3.tar.gz
3. $ tar -zxvf cnD-1.3.tar.gz
   

   cnD/
   cnD/COPYING
   cnD/Makefile
   cnD/README
   cnD/bin/
   cnD/bin/cnD
   cnD/bin/cnD.x86-64
   cnD/bin/pileup2win.pl
   cnD/bin/extractCNChanges.pl
   cnD/bin/extractCNFromVit.pl
   cnD/bin/metaCaller.pl
   cnD/cnD/
   cnD/cnD/CNVModel.d
   cnD/cnD/BinData.d
   cnD/cnD/Common.d
   cnD/cnD/Estimator.d
   cnD/cnD/cnD.d
   cnD/cnD/JointCNVDistribution.d
   cnD/cnD/ModelParameters.d
   cnD/cnD/StateSummary.d
   cnD/dhmm/
   cnD/dhmm/Alphabet.d
   cnD/dhmm/Distribution.d
   cnD/dhmm/HmmAlgorithms.d
   cnD/dhmm/MarkovModel.d
   cnD/dhmm/State.d

4. Copy README for web page
   $ mkdir /U:/simonlabweb/bioinformatics/programs/cnd
5. $ cp cnD/README /U:/simonlabweb/bioinformatics/programs/cnd/README.txt
6. Manual install
   $ cd cnD/bin
7. $ cp -puv *pl cnD /usr/local/bin/
   `extractCNChanges.pl' -> `/usr/local/bin/extractCNChanges.pl'
   `extractCNFromVit.pl' -> `/usr/local/bin/extractCNFromVit.pl'
   `metaCaller.pl' -> `/usr/local/bin/metaCaller.pl'
   `pileup2win.pl' -> `/usr/local/bin/pileup2win.pl'
   `cnD' -> `/usr/local/bin/cnD'
8. Cleanup
   $ cd ../..
9. $ rm cnD -rf