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
- gdc
- Ubuntu was easy:
$ sudo apt-get install gcd
- But not needed, cnD includes a pre-compiled binary, why don't the instructions say this?
- Tango
- $ sudo yum install tango-devel
- Set::IntSpan Perl module
- $ sudo cpan Set::IntSpan
Installation
- $ cd /programinstallers/
- $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/cnd/cnD-1.3.tar.gz
- $ 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
- Copy README for web page
$ mkdir /U:/simonlabweb/bioinformatics/programs/cnd
- $ cp cnD/README /U:/simonlabweb/bioinformatics/programs/cnd/README.txt
- Manual install
$ cd cnD/bin
- $ 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'
- Cleanup
$ cd ../..
- $ rm cnD -rf