installing pipe2:

Check if you have java on your machine.
If not, then see below (*).
Check your java version.
 
To check your java version in windows: 
  go to start, then run (or in vista use the search area in the start menu).
  fill in: 
  cmd <enter>
  java -version <enter>
  If you have java installed, it will now display your java version.
  the java version should be at least 1.6 to let pipe2 work properly.

For macs:
  Default installed java version is to old. Use the magnifier glass in the upper right corner,
  search for "java preferences". Use this application to check the current active version.
  If the version is to low (under 1.6) install a newer version, and go back to the java preferences.
  Now drag the newest java version to the top of the list.


(*) If you don't have java or an old version, please go to
  http://www.java.com




Once you have the correct java version, go to

http://sourceforge.net/projects/pipe2/files/Pipe%202/PIPE2%20V2.5/pipe25_rc5.zip/download

A pop up screen will ask you to download pipe2. Download pipe2 (pipe25_rc5)

If this doesn't work:
  Go to http://sourceforge.net/projects/pipe2/
  Select "View all files"
  Open the map Pipe 2
  Then the map Pipe2 V2.5
  And download the pipe25_rc5.zip file.

Note that we use pipe2.5 and NOT pipe3. This is because some modified files and modules might not work properly in pipe3.

Now open the downloaded file with winzip or winrar or similar programs,
and extract/move the map pipe25_rc5 to the directory of your choice.

module extensions and fixes:
go to 

http://tinyurl.com/pipe2extramodules

download the pipe2mods.zip file
open it, and place the files in the following places:

place DataLayer.class and Place.class in ../pipe25_rc5/pipe/dataLayer
replace the original files here

place the folders CapToOne, minimalSyphoins and processes in ../pipe25_rc5/pipe/modules
delete the old minimalSyphon map first, or overwrite it

to run pipe:
open the file "pipe" in ../pipe25_rc5
In windows, you can make a shortcut of the file by right clicking, and placing it at a more accessible location.