This page was last updated on Wednesday, 22-Jan-2014 16:11:25 CST

Installation notes for SMRT Analysis Software version 2.0.1

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Prerequisites

• SMRT® Analysis is only supported on:
  • English-language Ubuntu 10.04
  • English-language RedHat/CentOS 5.6
  • By request English-language Ubuntu 8.04 and RedHat/CentOS 5.3 are temporarily supported as well.
• Set up an Ubuntu 10.04 Virtual Machine in VirtualBox
• Perl modules:
  $ sudo cpan Statistics::Descriptive
• $ sudo cpan XML::LibXML
• liblapack3gf install with apt-get failed, but I could install it with the graphical interface
• Same with libssl0.9.8, except it is already installed.
• $ sudo apt-get install mysql-server
• Sun Grid Engine - see http://pka.engr.ccny.cuny.edu/~jmao/node/49
  $ sudo aptitude install gridengine-client gridengine-common gridengine-master gridengine-qmon
• My grid is just this one computer, so against the rules also install:
  $ sudo aptitude install gridengine-exec
• $ sudo apt-get install openmpi-common
• $ sudo qmon

Installation in the virtual machine

1. Create a user smrtanalysis with sudo privileges to do the install
2. Log in as smrtanalysis for following steps
3. $ cd /programinstallers/
4. $ wget -N programs.pacificbiosciences.com/l/1652/2013-06-04/2t28zc
5. Change permissions temporarily on /opt
   $ sudo chmod 777 /opt
6. $ tar -C /opt -xvvzf smrtanalysis-2.0.1-centos-5.6.tgz
7. $ ln -s /opt/smrtanalysis-2.0.1 /opt/smrtanalysis
8. Change permissions back
   $ sudo chmod 775 /opt
9. $ cd /opt/smrtanalysis
10. Edit /opt/smrtanalysis/etc/setup.sh to match your installation location
    $ sudo nano /opt/smrtanalysis/etc/setup.sh
    (No change needed, using default install location)
11. $ sudo /opt/smrtanalysis/etc/scripts/postinstall/configure_smrtanalysis.sh
12. $ sudo /opt/smrtanalysis/etc/scripts/tomcatd start
13. $ sudo /opt/smrtanalysis/etc/scripts/kodosd start
14. Move data storage location to folder outside virtual machine
    $ mv /opt/smrtanalysis/common/userdata.d /dcshare/pacbio/
15. Deleted now-empty folder
    $ sudo rmdir /opt/smrtanalysis/common/userdata.d
16. $ sudo ln -s /dcshare/pacbio/userdata.d /opt/smrtanalysis/common/userdata.d
17. Allow access to shared directory outside virtual machine (not sure if necessary for www-data)
    $ sudo usermod -a -G vboxsf smrtanalysis
    $ sudo usermod -a -G vboxsf www-data
18. I moved the references back on the virtual machine, otherwise uploads failed accessing the references/index.html file even though permissions seemed okay
19. Access the SMRTPortal at http://localhost:8080/smrtportal
20. $
21. $
22. $
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24. $
25. $
26. From http://seqanswers.com/forums/showthread.php?t=27472
    • $ which python
      /usr/bin/python
    • $ source /opt/smrtanalysis/etc/setup.sh
    • $ which python
      /opt/smrtanalysis/redist/python2.7/bin/python