Path - FAQ & Trouble-shooting:


FAQ:

Trouble-shooting Table:


FAQ:

What is Path?

  • The Path web application is a first-step bioinformatics approach to investigate gene-gene interactions in genetic association studies.

Why use Path?

  • Path is designed to help you:
    • Interface your SNP data with biological information from several online bioinformatics databases.
    • Generate biologically plausible hypotheses for testing gene-gene interactions.
    • Select a subset of SNPs and conduct SNP-SNP interaction tests.
    • Store analysis results.
    • Explore analysis results through interactive plots and summary tables.

How do I install Path?

What do I need to run Path?

  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 before running Path.
  2. Install the UNPHASED software that comes bundled with Path. To do this, extract the files within the unphased-3.0.13 archive. Three directories will be created: bin/ containing executable files (unphased.sol is a Solaris 10 binary, unphased.lnx a Linux binary, and unphased.exe a Windows binary), doc/ containing documentation files, and src/ containing the source code. Make sure to include the location of the UNPHASED executable file in your PATH environment variable. Path currently supports version 3.0.13 of UNPHASED. On some systems, the precompiled binaries of UNPHASED may not work and it may be necessary to build the UNPHASED program from source with a make utility.
  3. It’s a good idea to install the latest version of your default internet browser, as well.

How do I run Path?

  1. First, you need to set up a database for Path by running the Path Setup application. To run the Path Setup application, first navigate to the Path folder, then execute the runSetup.bat (for Windows) or runSetup.sh (for Linux) file. Linux users may need to change the permission of the runSetup.sh file in order to allow it to execute. This can be done by entering the following command: chmod +x runSetup.sh

  2. After setting up your database with the Path Setup application, you must close the Path Setup application. You can then run Path by executing the runPath.bat (for Windows) or runPath.sh (for Linux) file. Linux users may need to change the permission of the runPath.sh file in order to allow it to execute. This can be done by entering the following command: chmod +x runPath.sh
    Please note that it is only possible to have one installation of Path running at any time, although you may have multiple Path tabs or windows open in your browser.

How do I set the JRE_HOME environment variable?

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=/usr/Java/jre1.6.0_13/lib
      where /usr/Java/jre1.6.0_13/lib should be replaced with the path to where Java is installed on your machine.
    • If you are planning on running Path in an already open terminal window, reload your .bashrc via a command like:
        source path/to/your/.bashrc

How do I add UNPHASED to my PATH environment variable?

In Windows:

  • First, check to see if UNPHASED 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 “unphased” in the console window.
    • If the command is not recognized, UNPHASED needs to be added to the PATH environment variable.

  • To add UNPHASED’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 line like this to the variables value, changing it to reflect the location of UNPHASED on your system:
        ;C:\unphased-3.0.13\bin

In Linux:

  • First, check to see if UNPHASED is already added:
    • Open up a terminal window.
    • Type “unphased” into the terminal.
    • If the command is not recognized, UNPHASED needs to be added to the PATH environment variable.

  • To add UNPHASED’s location to PATH:
    • Run “echo $PATH” in a terminal.
      • Go to one of these directories (i.e. /usr/local/bin) and create a symbolic link to UNPHASED as follows:
        • ln -s /your/path/to/UNPHASED/executable ./unphased
    • Or, add a line like this to your .bashrc:
        export PATH=$PATH:/your/path/to/UNPHASED/goes/here

How do I run multiple installations of Path simultaneously?

  1. First, make a copy of the Path directory and paste it wherever you wish.

  2. Second, open the copied Path folder and navigate to tomcat/conf/.

  3. Now, open the file “server.xml” with a plain text editor (i.e. Notepad, WordPad, Vim, TextEdit in plain text mode).

  4. Next, add 1 to all the port numbers in the file (i.e. change the line <Server port="8005" shutdown="SHUTDOWN"> to <Server port="8006" shutdown="SHUTDOWN">). This makes them different from the first installation of Path.

  5. Then, runPath.vbs (Windows) / runPath.sh (Linux) needs to be modified to reflect these changes.
    • For Windows, change the last line in runPath.vbs:
        WebSh.Run "http://localhost:8080/Path"
      to:
        WebSh.Run "http://localhost:8081/Path"
    • For Linux, change the last line in runPath.sh:
        'http://localhost:8080/Path'
      to:
        'http://localhost:8081/Path'

  6. Now, open up the file .../Path/tomcat/webapps/derby/WEB-INF/web.xml and add change the port number “1527” to something else (i.e. 1528).

  7. Then, open up the file .../Path/tomcat/conf/Catalina/localhost/Path.xml and change the number “1527” to the same port number (i.e. 1528).

  8. Finally, test the new installation of Path by running it as normal. If it doesn’t work, and the browser gives an error message stating that a particular port has already been assigned, then change the server.xml, web.xml, Path.xml and runPath.bat/.sh files again to use different port numbers.

Do I need an internet connection to run Path?

  • Yes, in order for the Path web application to work fully an internet connection is required. You may still run Path without access to the internet, but certain features that fetch data from online resources may not work altogether.

  • The Path Setup application needs an internet connection during the registration process, while fetching data from online resources, and when updating kegg pathways, gene links, and gene aliases.

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 Path up.

Problem

Possible Solutions

Path web application looks odd in internet browser.
  • Upgrade to a more recent version of browser.

  • Enable Java plug-in in browser.

  • Enable JavaScript in browser.

  • Enable load images automatically option in browser.

  • Download a more web standards-compliant browser, such as Firefox.

Upon running runPath.bat / runPath.sh a(n):
  • “Error 404: Page not found” appears in browser.

  • “Failed to Connect” error appears in browser.

    Tomcat has not started up yet:

  • Click refresh button in browser a couple of times.

  • Ensure that console window labelled “Tomcat” is still open; if not, double-click on runPath.bat (Windows) or runPath.sh (Linux) again.

  • If the console window labelled “Tomcat” is open, keep waiting since Tomcat hasn’t started up yet...

Upon running runPath.bat / runPath.sh an error message appears in browser stating that port 8080 (or port XXXXX) is already in use.
    Another application is already using that port:

  • Make sure that Path is not already running.

  • Find out what application could be using that port already and close it.

  • Refer to FAQ question How do I run multiple installations of Path simultaneously? for information on changing the port numbers that the Path web application uses.

Error window pops up stating database ‘pathDB’ failed to start.
    Another application is already using the database:

  • Make sure that all other instances of Path and Path’s database setup application are closed and restart the application.

  • Close all applications using Java, then force quit all Java processes called ‘java.exe’br>

    In Windows:

    1. Press Control-Alt-Delete to open the Task Manager.

    2. Under the ‘Applications’ tab, make sure Path and Path's setup application are not running.

    3. Click on the ‘Processes’ tab.

    4. Sort the processes by name.

    5. End all processes titled ‘java.exe’ by selecting the process, then clicking the ‘End Process’ button.

    6. Read the warning dialogue that pops up, then click the 'Yes' button to terminate the process.

    In Linux:

    1. Open a terminal window.

    2. Run the command “ps -e | grep java”.

    3. Kill all the java processes shown using “kill xxxx”, where xxxx is the 4-digit Process ID (PID).


  • Alternatively, restart your computer.

On the Gene List page, the words “no image” appear under the column header “LD Plot”.
  1. Close Path.

  2. Run Path’s database setup application (runSetup.bat / runSetup.sh).

  3. Click on the “Update” panel.

  4. Click the button labelled “Make LD Plots”.

  5. Close the Path Setup application.

During the registration process, just after submitting an email for registration, an error window pops up stating “Error: could not send registration details...”.
  1. Click OK to exit the application.

  2. Verify that you have access to the internet.

  3. Make sure that your firewall is not blocking the Path setup application.

  4. The Path registration server could be down. Try to register again, later.

  5. For downloads prior to 13 March 2009: Download a new version of Path, or try entering a name without any spaces in the “Name” field when registering.

  6. See the Contact Page.

For Linux: Something appears to be wrong with runSetup.sh/runPath.sh .
  • Try running Path from the terminal.

  • Make sure that the directory path to Path doesn’t contain any spaces, then change the line:

      export CATALINA_OPTS="-Dderby.system.home='/database' -Dunphased.home='/unphased.sh' -Dpath.home='$PWD'"

    to
      export CATALINA_OPTS="-Dderby.system.home=/database -Dunphased.home=/unphased.sh -Dpath.home=$PWD"

  • Open the shell script in a Unix text editor and check for Windows carriage returns (CTRL-M) at the end of each line; delete them if present, or download runPath.sh or runSetup.sh again.

  • If you have not already done so, install Java.

  • Make sure that Java is included in your $PATH environment variable:
    • Open a terminal window.
    • Type 'java' (without quotes) and hit enter.
      • If an error message states that 'java' doesn’t exist, you need to add it to $PATH.
        • One way is to add a line like this to your .bashrc:
            export PATH=$PATH:/path/to/java/jre1.6.0_12/bin

  • If upon running runPath.sh, an error message appears stating that the environment variables JRE_HOME or JAVA_HOME need to be set to run the application:
    • Add a line to your .bashrc following the format below:
    • export JRE_HOME=/path/to/java/jre1.6.0_12

  • If runSetup.sh won’t run, stating: “Error occurred during initialization of VM”, “Could not reserve enough space for object heap”, or similar:
    1. Open the file runSetup.sh with a Unix text editor.
    2. Find the line that looks like:
        java -Xms48m -Xmx1024m ... (etcetera)
    3. The numbers 48 and 1024 denote the minimum and maximum amount of memory to be available to the Java VM (virtual machine).
    4. Change the number 1024 to be less than your total amount of memory. For example, if you have 1GB of RAM change this number to 512.
    5. Save the file, and try running runSetup.sh again.

You have reason to believe that your database is corrupted (i.e. you accidentally deleted some files under “database”; the database is throwing many, many exceptions when called by the Setup application...)
  1. See if cleaning the database helps.

  2. Download a new copy of the database folder here and replace the old one.

When trying to run Path’s Setup application, an error occurs, stating that “JRE_HOME” or “JAVA_HOME” must be set.
You ran the Path Setup application’s allelic/genetic association test, but the test results are blank in Path’s SNP Summary page. You may have noticed that a lot of exceptions about “UNPHASED” were thrown in the Path Setup application’ console window.
    Install the UNPHASED software that comes bundled with Path. To do this, extract the files within the unphased-3.0.13 archive. Three directories will be created: bin/ containing executable files (unphased.sol is a Solaris 10 binary, unphased.lnx a Linux binary, and unphased.exe a Windows binary), doc/ containing documentation files, and src/ containing the source code. Make sure to include the location of the UNPHASED executable file in your PATH environment variable. Path currently supports version 3.0.13 of UNPHASED. On some systems, the precompiled binaries of UNPHASED may not work and it may be necessary to build the UNPHASED program from source with a make utility.
Path runs as expected in Windows, but it is always necessary to refresh the start-up page a few times before Path displays in your browser.
  • Edit the line:

      wscript.sleep(500)

    to:
      wscript.sleep(XXXX)

    where XXXX is a time in milliseconds > 500. This is the amount of time the script waits for Tomcat to load before trying to access the Path web application via your browser.
When trying to compile UNPHASED from source I get the error:

In file included from UnphasedOptions.h:29, from UnphasedOptions.cpp:27: getline.h:27:22: error: iostream.h: No such file or directory make: *** [UnphasedOptions.o] Error 1
  • Open the getline.h file in the unphased source folder and change the line "#include <iostream.h>" to "#include <iostream>"


  • Open the LinkageData.cpp file in the unphased source folder and add the line "#include <cstring>" to the start of the file.