UPDATE: The TPP now includes Apache and configures it out of the box, so this is no longer applicable. For reference the original instructions are listed below.

Original Instructions

Here's how to run the ISB's Trans Proteomic Pipeline (TPP) with the Apache web server, as opposed to IIS. Prior to installing the TPP do this:

1. Create the "C:\Inetpub" and "C:\Inetpub\wwwroot" directories.
2. Download Apache 2.0
3. Install Apache using the default installation options.
4. Edit the Apache configuration file: C:\Program Files\Apache Group\Apache2\conf\httpd.conf
5. Add the following to the bottom of the file:

   Alias /isb-bin "C:/Inetpub/isb-bin"
   
   <Directory "C:/Inetpub/isb-bin">
       Options Indexes MultiViews
       AllowOverride None
       Order allow,deny
       Allow from all
   </Directory>
   
   Alias /tpp-bin "C:/Inetpub/tpp-bin"
   
   <Directory "C:/Inetpub/tpp-bin">
       Options Indexes MultiViews ExecCGI
       AllowOverride None
       Order allow,deny
       Allow from all
   
       AddHandler cgi-script .cgi .pl
       ScriptInterpreterSource Registry
   
       PassEnv WEBSERVER_ROOT
   </Directory>
   
   Alias /ISB "C:/Inetpub/wwwroot/ISB"
   Alias /isb "C:/Inetpub/wwwroot/ISB"
   
   <Directory "C:/Inetpub/wwwroot/ISB">
       Options Indexes MultiViews Includes
       AllowOverride None
       Order allow,deny
       Allow from all
   
       AddType text/html .shtml
       AddHandler server-parsed .shtml
   
       PassEnv WEBSERVER_ROOT
   </Directory>

6. Restart the Apache service so it picks up the new configuration.
7. Now install the TPP following the normal instructions. Skip the IIS specific configuration steps.
8. After installing the TPP find a .pl Perl script file in "C:\Inetpub\tpp-bin"...
   1. Right-click on the file and select "Open With... -> Choose Program"
   2. Select "Always use the selected program to open this kind of file"
   3. Click the "Browse..." button.
   4. Select "c:\cygwin\bin\perl.exe" and click OK.
   5. Click OK to close the dialog box. This ensures Apache will run Perl scripts using the Cygwin Perl interpreter.

That's it. Pasting in the Apache config is almost easier than configuring IIS using its user interface.