Member Since: Jun 25, 2005
Location: On the road
Mac Specs: 2011 MBP, i7, 16GB RAM, MBP 2.16Ghz Core Duo, 2GB ram, Dual 867Mhz MDD, 1.75GB ram, ATI 9800 Pro vid
05-13-2010, 05:03 PM
It sounds like what you are being told is to add the path where cufflinks and cuffcompare are located to your PATH environment variable. This is done so that you can just type either of those names in the Terminal and the system can find them and execute them. Otherwise you have to type the full path to execute those executables.
How you set the path is dependent on the shell being used. The default shell for OS X is now Bash. To add a path to the PATH environment variable is done like this;
When you type a command that resides in that last path, you no longer have to type the whole path. Note also, that the shell searches through the paths in the order that they appear. This is important to know when you have two commands with the exact same name.
Do a 'man bash' in the Terminal and look under the 'INVOCATION' section. You'll note that if you add your export command to one of three possible login shell files, that you will not have to type that command every time you start the shell.
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