Path2 FAQ


Path2 - FAQ & Trouble-shooting:






FAQ:

Trouble-shooting Table:




FAQ:

What is Path2?

  • Path2, a Java desktop application, is a first-step bioinformatics approach to investigate gene-gene interactions in genetic association studies. The first tab in the application, the “Import Data” tab, is basically a graphical front-end to PLINK to produce binary PLINK files. The second tab, the “Analysis Options” tab, runs PLINK analysis of imported data via the “Single SNP Association Analysis Options” and uses a combination of Perl and R scripts to perform genetic pathway analyses via the “Pathway/Ontology Association Analysis Options”.

Why use Path2?

  • Path2 is designed to help you easily perform:
    • PLINK-based single-SNP association analyses (logistic/linear regressions, family-based analyses)
    • Pathway/Ontology association analyses, including:
      • SNP Ratio Tests
      • SNP Permutation Tests
      • Nyholt Pathway Tests
      • Sidak Pathway Tests
      • Association LIst Go (gene ontology) AnnoTatOR (ALIGATOR) Tests

How do I install Path2?

What do I need to run Path2?

  1. Download the latest version of the Java Runtime Environment at www.java.com, and make sure the JRE_HOME environment variable is set to its location.

  2. You will need to download the latest version of PLINK (currently v1.07 built 10 August 2009) from http://pngu.mgh.harvard.edu/purcell/plink/, and make sure it’s location is included in your PATH environment variable.
  3. You will need to download the latest version of Perl (for ex. v5.10.1 built 24 August 2009) from http://www.activestate.com/perl, and make sure it’s location is included in your PATH environment variable. You will also need a bunch of Perl modules; versions tested with Path2 are in brackets:
    1. Parallel::ForkManager
    2. File::Basename
    3. Storable
    4. POSIX
    5. List::Util
    6. Proc::Background
    7. Cwd
    8. Term::ProgressBar
  4. You will need to download the latest version of R (for ex. v2.92 built 24 August 2009) from http://www.r-project.org/, and make sure it’s location is included in your PATH environment variable.

  5. It’s a good idea to install the latest version of your default internet browser, as well.

How do I run Path2?

  • Extract the archive, then just “open” (meaning run) the Java JAR file Path2.jar within. That’s it!

How do I set the JRE_HOME environment variable?

*Please note that this may not be necessary in Path2; use the following information only if an error occurs*

In Windows:

  • First, check to see if JRE_HOME is already set:
    • Press Start->Run... in the Start Menu. Or, press CTRL-ALT-DEL to open up the Task Manager and click File->New Task (Run...). Or, press Windows Key-R.
    • Enter “cmd” (without the quotes) in the box.
    • Type “echo %JRE_HOME%” in the console window.
    • If “%JRE_HOME%” is printed, JRE_HOME needs to be added to your environment variables.
  • To add JRE_HOME to your environment variables:
    • Press Start->Control Panel.
    • Double-click on System in the Control Panel’s Classic View.
    • Click on the Advanced Tab->Environment Variables in the System Properties box.
    • Click New under User (or System) Variables, and give the new variable the name JRE_HOME and a value similar to the following (changing it to reflect the location of Java on your system):
        C:\Program Files\Java\jre6

In Linux:

  • First, check to see if JRE_HOME is already set:
    • Open up a terminal window.
    • Type “echo $JRE_HOME” into the terminal.
    • If a blank line is printed, JRE_HOME needs to be added to your environment variables.
  • To add JRE_HOME to your environment variables:
    • Add a line like this to your .bashrc:
        export JRE_HOME=/your/path/to/java/goes/here
    • If you are planning on running Path2 in an already open terminal window, reload your .bashrc via a command like:
        source path/to/your/.bashrc

How do I add PLINK / R / Perl (“the program”) to my PATH environment variable?

In Windows:

  • First, check to see if the program is already added:
    • Press Start->Run... in the Start Menu. Or, press CTRL-ALT-DEL to open up the Task Manager and click File->New Task (Run...). Or, press Windows Key-R.
    • Enter “cmd” (without the quotes) in the box.
    • Type “plink” (for ex.) in the console window.
    • If the command is not recognized, the program needs to be added to the PATH environment variable.
  • To add the program’s location to PATH:
    • Press Start->Control Panel.
    • Double-click on System in the Control Panel’s Classic View.
    • Click on the Advanced Tab->Environment Variables in the System Properties box.
    • Scroll down under System Variables and select “PATH”.
    • ** WARNING! Be careful when editing PATH or you could break your operating system! **
    • APPEND (DO NOT REPLACE) a snippet like one of these to the variable’s value, changing it to reflect the location of the program on your system:
        ;C:\Plink\plink-1.07-dos
        ;C:\Perl\bin
        ;C:\Program Files\R\R-2.9.2\bin

In Linux:

  • First, check to see if the program is already added:
    • Open up a terminal window.
    • Type “plink” (for ex.) into the terminal.
    • If the command is not recognized, the program needs to be added to the PATH environment variable.
  • To add PLINK’s location (for ex.) to PATH:
    • Run “echo $PATH” in a terminal.
      • Go to one of these directories (i.e. /usr/local/bin) and create a symbolic link to PLINK as follows:
        • ln -s /your/path/to/PLINK/executable ./plink
    • Or, add a line like this to your .bashrc:
        export PATH=$PATH:/your/path/to/PLINK/goes/here

Can I run multiple installations of Path2 simultaneously?

  • Yes! Just make a copy of the Path2 directory and paste it wherever you wish. Running multiple instances of Path2 using the same installation is not supported.

Do I need an internet connection to run Path2?

  • Probably.... Path2 needs certain files from the internet in order to perform genetic pathway analyses. You may download these files yourself, then specify them in Path2. Or, if you have an internet connection you can just tell Path2 to download them in the “Import data” panel.



Trouble-shooting Table:

If you’ve read through the trouble-shooting table and still can’t find an answer to your problem, try referring to the FAQ and Tutorial to see if you missed something while setting Path2 up.

Problem

Possible Solutions

The Path2 application starts in the “Analysis Options” tab and can’t be switched back to the “Load Data” tab.
  1. Navigate to File->Clean Database and select it.
  2. This behaviour is on purpose; old data needs to be cleaned before new data can be imported.
When trying to run Path2 application, an error occurs, stating that “JRE_HOME” or “JAVA_HOME” must be set.
You ran the Path2 Setup application’s allelic/genetic association test, but you can’t find any results under “analysis\singlesnp\Combined\default”. Some exceptions may have been thrown in a console window, if you ran Path2 from one.
    You need to install PLINK in order to run Path2 association tests:
  1. Download and install a copy of PLINK.
  2. If you did not install PLINK to a location included in your PATH environment variable, see How do I add PLINK / R / Perl to my PATH environment variable?.
Nothing seems to happen when you run Pathway/Ontology Association Tests. I.e., you can’t see any results under the output folder you specified for them (default location is “analysis\pathway”).
    You need to install R and Perl for Path2’s Pathway tests to run correctly:
  1. Download and install a copy of R and Perl.
  2. If you did not install PLINK / R / Perl to a location included in your PATH environment variable, see How do I add PLINK / R / Perl to my PATH environment variable?.