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 PBJelly version 12.9.14

Home Page

Prerequisites

SMRT Analysis software (I have a virtual Ubuntu 10.04 machine for this)

Installation

  1. $ cd /programinstallers/
  2. $ wget -N http://downloads.sourceforge.net/project/pb-jelly/PBJelly_12.9.14.tgz
  3. $ cd /usr/local/bin
  4. $ tar -zxvf PBJelly_12.9.14.tgz
  5. $ ln -s PBJelly_12.9.14 PBJelly
  6. $ cd PBJelly_12.9.14
  7. $ nano exportPaths.sh
    ...
    export JELLYPATH=/usr/local/bin/PBJelly
    ...
        SEYMOUR_HOME="/opt/smrtanalysis"
    ...
  8. $ nano ~/.bashrc
    ...
    source /usr/local/bin/PBJelly/exportPaths.sh
  9. Log out and back in to test
    $ echo $PATH
    should end with :/usr/local/bin/PBJelly/
  10. Make sure we are using the right python
    $ which python
    should show /opt/smrtanalysis/redist/python2.7/bin/python