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

Installation notes for SVMerge version 1.2r37

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Prerequisites

• $ sudo cpan Set::IntSpan
• BreakDancerMax
• Pindel
• cnD
• SECluster - this is included in SVMerge
• bedtools
• samtools
• Exonerate
• rdxplorer is no longer supported

Installation

1. $ cd /programinstallers/
2. $ wget -N http://downloads.sourceforge.net/project/svmerge/Releases/SVMerge-1.2r37.tar.gz
3. $ mkdir /usr/local/bin/svmerge
4. $ cd /usr/local/bin/svmerge
5. $ tar -zxvf /programinstallers/SVMerge-1.2r37.tar.gz
   

   data/
   data/submat.txt
   docs/
   docs/SVMerge_Documentation.pdf
   README
   LICENSE.TXT
   example/
   example/example.config
   lib/
   lib/BamCheck.pm
   lib/ExonerateParse.pm
   lib/FilterSV.pm
   lib/LocalAssemble.pm
   lib/MergeSV.pm
   lib/ParseConfig.pm
   lib/ParseSV.pm
   lib/RunSVcallers.pm
   lib/RunSVcallers/
   lib/RunSVcallers/LSF.pm
   lib/RunSVcallers/SGE.pm
   bin/
   bin/makeNewProject.sh
   bin/samfilter.sh
   bin/splitFile.sh
   bin/coord2config.pl
   bin/filterAndMerge.pl
   bin/getSeqLines2.pl
   bin/makePindelv2fastq.pl
   bin/mergeFinalCalls.pl
   bin/parseBoundary.pl
   bin/runAlignParse.pl
   bin/runAssembly.pl
   bin/runParser.pl
   bin/runSVcallers.pl
   bin/SECluster.pl
   bin/svAssemble.pl
   bin/gcCorrect.pl
   bin/gcmedian.pl
   bin/tab2bed.pl

6. Make readable and executable
   $ chmod +r -R /usr/local/bin/svmerge
7. $ chmod +rx -R /usr/local/bin/svmerge/bin
8. Add this directory to default PATH
   $ sudo nano /etc/profile
   ...
   PATH="$PATH:/usr/local/bin/svmerge/bin"
   ...
9. Copy documentation for web page
   $ mkdir /U:/simonlabweb/bioinformatics/programs/svmerge
10. $ cp -puv docs/SVMerge_Documentation.pdf /U:/simonlabweb/bioinformatics/programs/svmerge/
11. $ chmod 666 /U:/simonlabweb/bioinformatics/programs/svmerge/SVMerge_Documentation.pdf