Pathway Tools OS X Stability Hacks

1. If Pathway Tools is running, close it either properly, or hold the "control" key while you press the "C" key repeatedly until you get a prompt similar to EC(1), then let go of the "control" key (and stop pressing the "C" key), then type:
   

   (exit)

   
   
   
   
2. Download and install XCode (you may need to register to download XCode). Alternatively, you may install XCode from your Apple OS X CD or DVD. NOTE: if you are downloading XCode, make sure that you download the correct version. If you are running OS X Snow Leopard, download XCode 3.2.2, if you are running OS X Leopard, download XCode 3.1.1. Please note that XCode is easily found on the MacPorts website (which we need anyways), hence I have used that website as a reference for finding XCode.
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
3. Open the XCode installer file (the screenshots show how to do this if you have downloaded XCode: hold the "control" click on the DMG file, then let go of the "control" key and click on "open", then open XcodeTools.mpkg in the window which pops up).
   
   
   
   
   
4. Proceed through the instatllation process
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
5. Go back to the MacPorts website and download the appropriate MacPorts for your OS X
   
   
   
   
   
   
   
   
   
   
   
6. Double Click on the pkg file in the window which pops up, and proceed through the installation process:
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
7. Run the mac_hackpatch file included with koala (note you may need to type your password a few times for this script; additionally, this script takes a while to run - it may be a good time to go for a coffee break)
   
   
   
   
   
   
   
   
   
8. Open a terminal
   
   
   
   
   
   
   
   
   
   
   
9. Restart pathway tools. NOTE: you may still receive an error regarding libScipAll.so, if you are using OS X 10.5 (Leopard). Please disregard this error, as there is nothing we can do about it at the present time; additionally, no loss of stability has been observed by this error by our group at the time of this writing - August 31, 2012.
   
   
   
   
   
10. You may wish to close pathway tools now and return to the starting the web server page (i.e. use "./pathwaytools -www" instead of "./pathwaytools" in the above screenshot. (Click here to return to starting Pathway Tools Webserver)