You will have downloaded the EMBOSS and EMBASSY packages to a suitable directory. For this example we will assume you have downloaded them to /packages so you should now have the following files (or similar) and maybe more packages in EMBASSY.
% ls EMBOSS-1.0.0.tar.gz PHYLIP-3.573c.tar.gz MSE-0.0.4.tar.gz TOPO-0.1.tar.gzFirst unpack the EMBOSS distribution
% gunzip EMBOSS-1.0.0.tar.gz % tar xf EMBOSS-1.0.0.tarThis will create a new directory, EMBOSS-1.0.0 or similar. You may wish to use tar xpf for unpacking EMBOSS.
Enter the EMBOSS directory
% cd EMBOSS-1.0.0create a directory for the EMBASSY packages
% mkdir embassyNow copy the EMBASSY packages to the EMBASSY directory
% cp ../MSE-0.0.4.tar.gz PHYLIP-3.573c.tar.gz \ TOPO-0.1.tar.gz embassyGo into the EMBASSY directory and unpack those packages.
% cd embassy % gunzip MSE-0.0.4.tar.gz % tar xf MSE-0.0.4.tarand so on for each EMBASSY package.
Go back up one directory to the main EMBOSS package directory and prepare to start compilation.