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SMRT View

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fripp edited this page Oct 15, 2014 · 67 revisions

SMRT® View is an open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems.

  • You can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding.
  • You can also visualize base modifications, base identification and motifs analysis results.

SMRT View - v2.3.0 Released (Standalone)

This version includes several new useful features for human data sets, and is 100% compatible with v2.X data.

Downloads

Documentation

Installing SMRT View on Mac OS

Note: SMRT View requires the following:

  • Mac OS 10.6 or later.
  • Apple Java: Java for OS X 2013-004 (1.6.0_51-b11-457-10M4509) or later.
  • A minimum of 4 GB of RAM and approximately 250 MB of disk space, which includes around 150 MB for Java.

  1. Extract the contents of the compressed distribution archive:

    Unzip smrtview_2.3.0.140936_macos.gz to your Applications folder. Note: SMRT View will work only from the Applications folder.

  2. Start SMRT View and view data:

    a) Double-click the SMRT View application.

    b) Choose File > Open Data From Server and navigate to the location of your data.

    c) Select the metadata.rdf file associated with the SMRT Portal job to visualize.

    d) Click OK. SMRT® View displays a message with the name of the reference file for this data.

    e) Select the reference.info.xml file for the reference to use and click OK. SMRT® View displays your data.

####Customization####

When you browse using File > Open Data From Server, the configuration script defaults to the root directory. You can change the default to a different location by following these steps:

a) Close all instances of SMRT View.

b) Use a text editor or Terminal to open the SMRT View Desktop startup script file, located here: /Applications/SMRTView.app/Contents/MacOS/SMRTView.

c) Edit the SMRTVIEW_HOME variable.

You can also modify the file and launch it directly in Terminal to open multiple instances of SMRT View, open specific data sets, references and tracks. Note that the script also handles starting and stopping the server.

###Installing SMRT View Desktop on Linux ###

Note: SMRT View requires the following:

  • Minimum Linux Versions: Red Hat Linux 6.x and above; Ubuntu Linux 10.04 and above; Suse Linux 11.x and above.
  • Oracle Java: Java Version 7 Update 25 or later for Linux.
  • A minimum of 4 GB of RAM and approximately 280 MB of disk space, which includes around 180 MB for Java 7.

  1. Extract the contents of the tarball:

    a) Copy the smrtview tarball to a directory of your choice. Example: /common/apps/pacbio.

    b) CD to that directory and extract the content of the compressed archive using the following command: tar -zxpvf smrtview_2.3.0.140936_linux.tar.gz. The tarball contains one root directory, smrtview-2.3.0, which contains all applications, libraries and test data. The full path to the smrtview-2.3.0 directory, e.g. /common/apps/pacbio/smrtview-2.3.0, is the program variable SEYMOUR_HOME (see below).

  2. Update the configuration files:

    a) Change the current directory to the bin directory. Example: cd /common/apps/pacbio/smrtview-2.3.0/bin.

    b) Launch the linux_configure script from within the bin directory by typing ./linux_configure. The script determines the hostname, home directory and http port, and asks for confirmation. If the configuration is correct, press Enter to continue.

    If the configuration data is not correct, edit the script, and change the corresponding environment variables. You can run the script multiple times if the installation configuration changes.

    After the configure script finishes, the system is ready to use.

  3. Start/Stop the server:

    a) To start the tomcat web server and SMRT View server: Go to /common/apps/pacbio/smrtview-2.3.0/bin and type ./smrtanalysis start. The command returns after printing a few messages; the server process is now running in the background. The server continues to run even after you log off the terminal session.

    b) To check if the web server is running by opening the manager web console in a web browser: Type http://hostname:8080/manager/html.

    The user name/password for the tomcat manager app are: smrtanalysis/smrtanalysis. You should see the smrtanalysis and smrtview apps listed.

    Note: It may take 30-60 seconds for the tomcat apps (including the manager app) to become available after the start command.

    To stop tomcat: Go to /common/apps/pacbio/smrtview-2.3.0/bin and type ./smrtanalysis stop.

  4. View data in SMRT View:

    • Local and remote host access: Use your web browser to install a shortcut to SMRT View. Select the "Install SMRT View on your computer" link on this page: http://hostname:8080/smrtview.
    • Local host access: Use the smrtview script to launch smrtview from the command line or terminal. Type ./smrtview for a list of options.

###Installing SMRT View on Windows###

Note: SMRT View requires the following:

  • Microsoft Windows 7 or later (64-bit version strongly recommended; 32-bit version is no longer recommended and in a future release will not be supported.)
  • Oracle Java: Java Version 7 Update 25 or later for Windows.
  • A minimum of 4 GB of RAM and approximately 350 MB of disk space, which includes around 250 MB for Java 7.

  1. Extract the contents of the compressed distribution archive: Unzip smrtview_2.3.0.140936_windows.zip to a directory on your system.

    Note: The full path of the destination directory cannot contain spaces. Example: c:\program files\pacbio will not work.

  2. Configure the application:

    a) Using Windows Explorer or a command prompt window, navigate to the \smrtview-2.3.0\bin directory.

    b) Start win_configure.bat and follow the instructions to configure SMRT View. This may take a few minutes. Rerun this .bat file if you move or rename the install directory, or if you change the computer name.

  3. Start SMRT View and view data:

    a) Double-click the SMRT View Desktop 2.3.0 shortcut.

    b) Choose File > Open Data From Server and navigate to the location of your data.

    c) Select the metadata.rdf file associated with the SMRT Portal job to visualize.

    d) Click OK. SMRT View displays a message with the name of the reference file for this data.

    e) Select the reference.info.xml file for the reference to use and click OK. SMRT View displays your data.

####Start and Stop the Server####

The configuration script creates a startup file, win_smrtview.bat, which by default starts the SMRT View server in a secondary window if it is not already running. The script also shuts down the server when the application closes. Edit the script to change this behavior as needed, and use the commands in the admin directory to control the server.

####Browsing Data####

When you browse using File > Open Data From Server, the configuration script defaults to the root of the drive where the software is installed. You can change this default to a different location:

a) Close all instances of SMRT View.

b) Open the following file: .\redist\tomcat\bin\catalina.bat.

c) Edit the SMRTVIEW_HOME variable.

####Customization####

  • You can also modify the file to open specific data sets by using SMRT view command line options to specify jobs, references and tracks.
  • By following the instructions above, you can also install SMRT View on a USB memory stick.

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