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

This page was last updated on Tuesday, 01-Dec-2015 11:49:43 CST

Installation notes for gasv version Release_Oct1_2013

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Prerequisites

Note that GASV and BAMToGASV are maintained in Java.
Executable jar files are built using ant, available
at: http://ant.apache.org/ant

Installation

  1. $ ver="Release_Oct1_2013"
  2. $ cd /programinstallers/
  3. $ wget -N https://gasv.googlecode.com/files/GASV$ver.tgz
  4. $ tar -zxvf GASV$ver.tgz
  5. $ cd gasv
  6. Optional, only if needed:
    $ export ANT_HOME=/usr/share/ant/
  7. Note that when the following commant prints out installing, it is actually just compiling, not installing
    $ ./install

    Installation complete. Check for errors.
  8. Manually install only needed files
    $ mkdir /usr/local/bin/gasv
  9. $ cp -puv bin/* scripts/* /usr/local/bin/gasv/
    `bin/BAMToGASV_AMBIG.jar' -> `/usr/local/bin/gasv/BAMToGASV_AMBIG.jar'
    `bin/BAMToGASV.jar' -> `/usr/local/bin/gasv/BAMToGASV.jar'
    `bin/convertClusters' -> `/usr/local/bin/gasv/convertClusters'
    `bin/GASV.jar' -> `/usr/local/bin/gasv/GASV.jar'
    `bin/GASVPro-CC' -> `/usr/local/bin/gasv/GASVPro-CC'
    `bin/GASVPro-graph' -> `/usr/local/bin/gasv/GASVPro-graph'
    `bin/GASVPro-HQ.sh' -> `/usr/local/bin/gasv/GASVPro-HQ.sh'
    `bin/GASVPro-mcmc' -> `/usr/local/bin/gasv/GASVPro-mcmc'
    `bin/GASVPro.sh' -> `/usr/local/bin/gasv/GASVPro.sh'
    `bin/SimpleSAMRecordParser.jar' -> `/usr/local/bin/gasv/SimpleSAMRecordParser.jar'
    `scripts/GASVPruneClusters.pl' -> `/usr/local/bin/gasv/GASVPruneClusters.pl'
    `scripts/parseLowQForNovoalign.pl' -> `/usr/local/bin/gasv/parseLowQForNovoalign.pl'
    `scripts/sortPR.bash' -> `/usr/local/bin/gasv/sortPR.bash'
  10. Add to default PATH
    $ sudo nano /etc/profile

    PATH="$PATH:/usr/local/bin/gasv"
  11. Copy documentation to local web page
    $ cp -puv README.txt RELEASE_NOTES.txt doc/GASV_UserGuide.pdf ../web/gasv/
  12. Cleanup
    $ cd /programinstallers && rm gasv -rf