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Installation and Upgrade Summary

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fripp edited this page Feb 9, 2013 · 34 revisions

Following are the steps for installing SMRT Analysis v1.4.0. For further details, click the links.

  1. Select an installation directory to assign to the $SEYMOUR_HOME environmental variable. In this summary, we use /opt/smrtanalysis.

  2. Decide on a sudo user who will perform the installation. In this summary, we use <thisuser>, who belongs to <thisgroup>. Note: The user installing SMRT Analysis must have sudo access.

  3. Extract the tarball and softlink the directories:

tar -C /opt -xvvzf <tarball_name>.tgz
ln -s /opt/smrtanalysis-1.4.0 /opt/smrtanalysis
sudo chown -R <thisuser>:<thisgroup> smrtanalysis-1.4.0
  1. Edit the setup script /opt/smrtanalysis-1.4.0/etc/setup.sh to match your installation location:
SEYMOUR_HOME=/opt/smrtanalysis
  1. Run the appropriate script:
  /opt/smrtanalysis/etc/scripts/postinstall/configure_smrtanalysis.sh
  • Option 2: If you are upgrading from v1.3.3 to v1.4.0 and want to preserve SMRT Cells, jobs, and users from a previous installation: Run the upgrade script.
  /opt/smrtanalysis/etc/scripts/postinstall/upgrade_and_configure_smrtanalysis.sh
  1. Set up distributed computing by deciding on a job management system (JMS), then edit the following files:
/opt/smrtanalysis/analysis/etc/cluster/<JMS>/start.tmpl
/opt/smrtanalysis/analysis/etc/cluster/<JMS>/interactive.tmpl
/opt/smrtanalysis/analysis/etc/smrtpipe.rc
/opt/smrtanalysis/redist/tomcat/webapps/smrtportal/WEB-INF/web.xml
/opt/smrtanalysis/analysis/etc/cluster/<JMS>/kill.tmpl

Note: If you are not using SGE, you will need to deactivate the Celera Assembler protocols so that they do not display in SMRT Portal. To do so, rename the following files, located in common/protocols:

RS_CeleraAssembler.1.xml to RS_CeleraAssembler.1.bak
filtering/CeleraAssemblerSFilter.1.xml to CeleraAssemblerSFilter.1.bak
assembly/CeleraAssembler.1.xml to CeleraAssembler.1.bak

  1. New Installations only: Set up user data folders that point to external storage.

  2. New Installations only: Set up SMRT Portal.

  3. Start the SMRT Portal and Automatic Secondary Analysis Services

  4. Verify the installation.

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