Pathway Tools Installation Guide -- Proxy Configuration

Set the environment variable PROXY to the name and port number of the proxy server (which you can obtain from your network administrator), separated by a colon.

Unix: We recommend setting up PROXY in the login script of the user who will be running Pathway Tools. Here is a fictitious example of an appropriate proxy entry in file ~/.login :
setenv PROXY amadeus.company.com:12345
Windows: This capability has not yet been tested on Microsoft Windows, but the file C:\AUTOEXEC.BAT may be a suitable place to set PROXY. (If this works for you, please let us know.) For example:
SET PROXY=amadeus.company.com:12345