Build the ViennaRNA Package

The installation location can be controlled through options to the configure script. E.g. to change the default installation location to the directory VRP in your $HOME/Tutorial directory use the -prefix tag so the compiler knows that the target directory is changed. When you add the term -witout-perl no super-user privileges are necessary, because the perl module of the package (RNA.pm) is not copied to a restricted system directory.

1. To configure and build the package just run the following commands.

   	  $ cd ViennaRNA-[2.1.1]
   	  $ mkdir -p ~/Tutorial/Progs/VRP
   	  $ ./configure --prefix=$HOME/Tutorial/Progs/VRP --without-perl
   	  $ make install
   

   You already know the cd and the mkdir command, ./configure checks whether all dependencies are fulfilled and exits the script if some major requirements are missing. If all is ok it creates the Makefile which then is used to start the buildingprocess via make install.
2. To install the ViennaRNA package system wide (only for people with superuser privileges, which we are NOT!) run

   	  $ ./configure
   	  $ make install
   

You find the installed files in

1. $HOME/Tutorial/Progs/VRP/bin (programs)
2. $HOME/Tutorial/Progs/VRP/share/ViennaRNA/bin (perl scripts)

Wherever you installed the main programs of the ViennaRNA Package, make sure the path to the executables shows up in your PATH environment variable. To check the contents of the PATH environment variable simply run

  $ echo $PATH

For easier handling we now create a folder containing all our binaries as well as perl scripts and copy them into a common folder.

  $ cd ~/Tutorial/Progs/
  $ cp VRP/share/ViennaRNA/bin/* .

Now you can show the contents of the folder using the command ls.

Also copy the binaries from the VRP/bin folder. In the next step we add the path of the directory to the PATH environment variable (e.g. use pwd) so we don't need to write the hole path every time we call it.

	  $ export PATH=$PATH:$HOME/Tutorial/Progs/

Note that this is only a temporary solution. If you want the path to be permanently added you need to add the line above to the config file of your shell environment. Typically bash is the standard. You need to add the export line above to the .bashrc in your homedirectory. To reload the contents of .bashrc type

	  $ source ~/.bashrc

or close the current terminal and open it again. (Remember, this works only for the bash shell.) To check if everything worked out try to get a brief description of a program e.g.

  $ RNAfold --help

If this doesn't work reread the steps described above more carefully.