Back to Windows Installation Instructions Table of Contents
If you use these install instructions, please cite: Graham G.M. Alvare, Natalie K. Björklund, John Schellenberg, Richard Sparling, Brian Fristensky; Koala: Overlaying Local Gene Expression Data on BioCyc Pathway Diagrams

Install Koala without installer

To go to the Koala installer instructions, Click here

  1. Download Koala


  2. Open the containing folder - use "right-click" (clicking with the right mouse button) to access this menu item


  3. Extract Koala from the zip file - use "right-click" (clicking with the right mouse button) to access this menu item












  4. Import koala.sql into your database server

  5. Copy the files under koala-biocyc to your pathway tools user home directory (by default this is C:\Documents and Settings\Your username\Application Data\ptools-local\html) - and change all references of localhost/koala and localhost%2Fkoala (the url-encoded version of localhost/koala - %2F is a '/' character) to your web server's address for koala

  6. Create or alter your ptools-init.dat file to contain the line:

    WWW-Html-Root-Dir C:\Documents and Settings\Your username\Application Data\ptools-local\html+C:\Program Files\Pathway Tools\aic-export\htdocs

    Where C:\Documents and Settings\Your username\Application Data\ptools-local\html is the path of your Pathway Tools user HTML directory, and C:\Program Files\Pathway Tools\aic-export\htdocs is the path of your Pathway Tools installation HTDOCS directory.

  7. Copy the contents of Koala-apache into your Apache web server's htdocs directory and alter the globals.php to use your database connection information

  8. Ensure your PHP version has MySQL and SSL enabled, and ensure that Apache supports .htaccess files

  9. Run the following command on the command line to generate a .htpasswd file for password protecting Koala. The .htpasswd file will reside in the same directory as the other Apache files, for alternate password protection, please see Apache documentation on .htaccess files)
    C:\Program Files\Apache Software Foundation\Apache2.2\bin\htpasswd.exe -bc Path to Koala's Apache files\.htpasswd username password

  10. You are now ready to start your Pathway Tools web server. Please see the following page for detailed instructions. If you get the following screen when starting your Pathway Tools web server, then you need to patch Pathway tools. Click here for instructions on how to patch pathway tools. Apply the patch, then proceed to the next step.