This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for SVDetect version r0.8b 2013/01/23

Home Page

Prerequisites

• Perl modules
  $ sudo cpan Config::General Tie::IxHash Parallel::ForkManager
• Optional components, described here: http://svdetect.sourceforge.net/Site/Download.html
  • Circos
  • SAMtools
  • BEDtools
  • UCSC Genome Browser

Installation

1. $ cd /programinstallers/
2. $ wget -N http://downloads.sourceforge.net/project/svdetect/SVDetect/0.80/SVDetect_r0.8b.tar.gz
3. $ tar -zxvf SVDetect_r0.8b.tar.gz
4. $ SVDetect_r0.8b
5. $ mkdir /U:/simonlabweb/bioinformatics/programs/svdetect
6. Installation (manually)
   $ cp -puv SVDetect_r0.8b/bin/SVDetect /usr/local/bin/
   `SVDetect_r0.8b/bin/SVDetect' -> `/usr/local/bin/SVDetect'
7. $ cp -puv SVDetect_r0.8b/scripts/* /usr/local/bin
   `SVDetect_r0.8b/scripts/BAM_preprocessingPairs.pl' -> `/usr/local/bin/BAM_preprocessingPairs.pl'
8. $ chmod +x /usr/local/bin/BAM_preprocessingPairs.pl
9. Copy file for web page
   $ cp -puv SVDetect_r0.8b/README /U:/simonlabweb/bioinformatics/programs/svdetect/README.txt
10. Cleanup
    $ rm SVDetect_r0.8b -rf