How do I do this manually?

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If you don't want to use use, you can of course apply the settings directly. This means essentially setting a few basic environment variables, the most important of which is PATH, which tells the system where to look for the commands that you issue or for the files that are used while executing something within a shell. You want to make your shell aware of some directories with system commands and shell commands in them.

Another environment variable that is often useful is MANPATH. This is for the Unix manual pages, and tells the system where to look for online-documentation.

Yet another one is LD_LIBRARY_PATH, which Is sometimes used by applications to find dynamic runtime libraries. The variable tells the runtime environment where to look for these, and your program might not run if LD_LIBRARY_PATH is not set correctly. If you experience problems with missing runtime libraries, try playing with LD_LIBRARY_PATH, otherwise it's best left unset.

For a csh, the the command to set environment variables is setenv:
where VARIABLE is the name of the environment variable, and VALUE is the value it is set to. This might be a number, or a string, in which case it should be enclosed by double quotes.

For ksh or bash the command is just the binary operator '=':
followed by the "export" command, which makes the variable part of the environment:
Note that for bash it is possible to place "export" in front of the variable assignment instead of issuing two separate commands:

To access the value of a environment variable, you have to type a "$" in front of it. For example you want to see which value your variable PATH has, you type:
echo $PATH
where echo is just a standard Unix command, and "$PATH" returns the value of PATH. The following command will append something to a previously defined variable (in a csh):
setenv PATH=$PATH":/yet/another/directory"
Here, "PATH" denotes the variable and "$PATH" denotes its present value.

Sometimes a variable needs to be reset for a specific application. It is then best to write a shell script that sets the variables and starts the application, rather than setting the variables globally in your startup files.

You can consult the configuration files of usepackage to find out which setting you need to apply to run a specific software or access certain features. The configuration is in
The syntax in that file is not hard to read, for instance the entry

>> blastwave : "Blastwave Solaris Packages" << 
blastwave * SunOS 5.* :
PATH += /opt/csw/bin,
MANPATH += /opt/csw/share/man,
INFOPATH += /opt/csw/share/info ;

tells us what directories to prepend to the environment variables PATH, MANPATH, and INFOPATH, respectively if we want to use "Blastwave".