Installing the Vienna RNA Package

For best portability the Vienna RNA package uses the GNU autoconf and automake tools. The instructions below are for installing the Vienna package from source. However pre-compiled binaries for windows users are available from the Vienna RNA home page, and pre-packaged version for linux and Mac OS may be availbale from other repositories.

Quickstart

Usually you'll just unpack, configure and make. To do this type:

	tar -zxvf ViennaRNA-1.6.tar.gz
	cd ViennaRNA-1.6
	./configure
	make
and (as root)
	make install

Install Paths:

The main programs, library, man, and info pages are installed in the usual places by default (i.e. /usr/local/{bin,lib,man,info}). In addition the following install paths are used:

header files    /usr/local/include/ViennaRNA    [includedir/ViennaRNA]
parameter files /usr/local/share/ViennaRNA      [datadir/ViennaRNA]
extra scripts   /usr/local/share/ViennaRNA/bin  [datadir/ViennaRNA/bin]
documentation   /usr/local/share/ViennaRNA/doc  [datadir/ViennaRNA/doc]

All these locations can be changed by calling ./configure with appropriate options. Examples:
If you don't have root access and thus can't install into /usr/local, run ./configure --prefix=$HOME/Programs/ to install everything in under the Programs directory in your home.

If you like having all software packages separated in their own directories you could run e.g.:

./configure --prefix=/opt/packages/ViennaRNA --datadir=/opt/packages/ViennaRNA

resulting in /opt/packages/ViennaRNA/{bin,lib,man,info,include,doc} directories

The installed location of the Perl module is determined by Perl's own configuration, independent of any configure options. To change the install path for the Perl module run e.g.

   cd Perl
   perl Makefile.PL PREFIX=$HOME/myperl5
   cd ..

after running the configure command.

Optional sub-packages

You can build the Vienna package without Perl support by running

   ./configure --without-perl

The programs AnalyseSeqs and AnalyseDists offer some cluster analysis tools (split decomposition, statistical geometry, neighbor joining, Ward's method) for sequences and distance data. To also build these programs add --with-cluster to your configure options.

This release includes the RNAforester and Kinfold programs, which can also be obtained as independent packages. Running ./configure in the ViennaRNA directory will configure those two packages as well. However, for detailed information and compile time options, see the README and INSTALL files in the respective subdirectories.

The Kinfold program can be used to simulate the folding dynamics of an RNA molecule, and is compiled by default. Use the --without-kinfold option to skip compiling Kinfold.

The RNAforester program is used for comparing secondary structures using tree alignment. To compile RNAforester you'll need to first install the g2 graphic library, then run configure with the --with-forester option.

The readseq program is not integrated in the build process. If desired, install readseq manually, following the instructions in the readseq directory.

Other configure options

Calculation of partition functions (via RNAfold -p) uses double precision floats by default, to avoid overflow errors on longer sequences. If your machine has little memory and you dont't plan to fold sequences over 1000 bases in length you can compile the package to do the computions in single precision by running ./configure --enable-floatpf.

Typing ./configure --help will give a complete list of all ./configure options and important environment variables. For more general information on the buid process see the INSTALL.configure file.

`Additional comments`



The maximum length of sequences that can be handled is limited by the
available memory on your computer. Memory requirements for folding a
sequence of length n will be approximately 12*n^2 bytes for RNAfold -p, and
4*n^2 bytes for the minimum free energy alone. 


There are man pages for all executables, the library is documented in
./man/RNAlib.texinfo. By default the RNAlib manual is installed in
info format. To produce an PDF or HTML version of the manual
type
   cd man
   make pdf
   make html

Most perl utilities contain embeded pod documentation which can be
displayed by typing e.g.  perldoc rotate_ss.pl .
Documentation in HTML can be found at http://www.tbi.univie.ac.at/~ivo/RNA/