Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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

Installation notes for cnD version 1.3 Feb 16, 2012

Home Page

Prerequisites

None

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