Installation

The ViennaRNA Package comes with a variety of executable programs and scripts as well as a C-library that provides access to our implemented algorithms. Moreover, the C-library is wrapped to scripting languages such as Perl 5 and Python.

Note

For best portability the ViennaRNA package uses the GNU autoconf and automake tools to prepare the compilation from source code. Read the Configuration section before you install our software if you intend to deviate from the default setup.

Installing from Source

The instructions below are for installing the ViennaRNA package from source. However, pre-compiled binaries for various Linux distributions, as well as for Windows users are available at the download section of the official ViennaRNA homepage.

See also…

Binary packages, Using conda, and Python interface only

Quick-start

Usually you’ll just download the latest source tarball, unpack, configure and make. To do this type:

tar -zxvf ViennaRNA-2.6.4.tar.gz
cd ViennaRNA-2.6.4
./configure
make
sudo make install

Installing from git repository

You can also get the latest source code from our git repository hosted at https://github.com:

git clone https://github.com/ViennaRNA/ViennaRNA.git

However, to proceed with the configuration and installation you need to perform some additional steps before actually running the ./configure script:

  1. Unpack the libsvm archive to allow for SVM Z-score regression with the program RNALfold:

tar -xzf src/libsvm-3.31.tar.gz -C src

  1. Unpack the dlib archive to allow for concentration dependency computations with the program RNAmultifold:

tar -xjf src/dlib-19.24.tar.bz2 -C src

  1. Install the additional maintainer tools gengetopt, help2man, flex, xxd, and swig if necessary. For instance, in RedHat based distributions, the following packages need to be installed:

    • gengetopt (to generate command line parameter parsers)

    • help2man (to generate the man pages)

    • yacc, flex and flex-devel (to generate sources for RNAforester)

    • vim-common (for the xxd program)

    • swig (to generate the scripting language interfaces)

    • liblapacke (for RNAxplorer)

    • liblapack (for RNAxplorer)

    • A fortran compiler, e.g. gcc-gfortran (for RNAxplorer)

  2. Finally, run the autoconf/automake toolchain:

autoreconf -i

After that, you can compile and install the ViennaRNA Package as if obtained from the distribution tarball.

Building the reference manual

Our implementations are documented with extra comments that are automatically parsed by doxygen. The extracted API documentation is then processed further by breathe and finally integrated into a comprehensive reference manual written in ReStructuredText. This manual is then usually compiled into HTML and PDF format by Sphinx.

We provide pre-compiled versions of the reference manual in our distribution tarballs and HTML versions at https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman and https://viennarna.readthedocs.io. However, under certain circumstances users might want to compile the reference manual themselves, e.g. when installing from git repository.

To succeed with the compilation the following tools are required:

  • doxygen (to extract the API documentation)

  • sphinx-build (to compile the manual)

  • pdflatex (to compile a PDF version of the manual)

In addition, we use the following sphinx extensions:

  • sphinx-multiproject

  • myst-parser

  • sphinx-copybutton

  • sphinxcontrib-bibtex

  • sphinx-rtd-theme

If all the above programs and python packages are available, compilation of the reference manual should succeed without any further problems.

Installation without root privileges

If you do not have root privileges on your computer, you might want to install the ViennaRNA Package to a location where you actually have write access to. To do so, you can set the installation prefix of the ./configure script like so:

./configure --prefix=/home/username/.local
make install

This will install the entire ViennaRNA Package into your home’s ~/.local/ directory that is commonly used for user-installed software. Just make sure that your PATH environment variable contains the $HOME/.local/bin directory such that our executables are looked-up for at the proper location.

Tip

The --prefix can be any other directory if you want to keep your installed software separate from each other. The make install command will then create the corresponding bin/, lib/, share/ directories within the directory you specified.

MacOS X users

Although users will find /usr/bin/gcc and /usr/bin/g++ executables in their directory tree, these programs are not at all what they pretend to be. Instead of including the GNU programs, Apple decided to install clang/llvm in disguise. Unfortunately, the default version of clang/llvm does not support OpenMP (yet), but only complains at a late stage of the build process when this support is required. Therefore, it seems necessary to deactivate OpenMP support, e.g.:

./configure --disable-openmp

See also…

OpenMP, Universal binaries, and Missing EXTERN.h

Using conda

The ViennaRNA Package is also available for the conda or mamba package manager. The only requirement is to set up the bioconda channels

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

and then you can easily install the viennarna bioconda package through

conda install viennarna

Binary packages

For convenience, we provide pre-compiled binary packages and installers for several Linux-based platforms, Microsoft Windows, and Mac OS X. They can be obtained from our official website.

Python interface only

The Python 3 interface for the ViennaRNA Package library is available at PyPI and can be installed independently using Python’s pip:

python -m pip install viennarna

Building the Python package

Our source tree allows for building/installing the Python 3 interface separately. For that, we provide the necessary packaging files pyproject.toml, setup.cfg, setup.py and MANIFEST.in. They are created by our autoconf toolchain after a successful run of ./configure. Particular default compile-time features may be (de-)activated by setting the corresponding boolean flags in setup.cfg. Running

python -m build

will then create a source distribution (sdist) and a binary package (wheel) in the dist/ directory. These files can be easily installed via Python’s pip.

Note

If you are about to create the Python interface from a fresh clone of our git repository, you require additional steps after running ./configure as described above. In particular, some autogenerated static files that are compiled into RNAlib must be generated. To do so, run

cd src/ViennaRNA/static
make
cd ../../..

Additionally, if building the reference manual is not explicitly turned off, the Python interface requires docstrings to be generated. They are taken from the doxygen xml output which can be created by

cd doc
make refman-html
cd ..

Finally, the swig wrapper must be build using

cd interfaces/Python
make RNA/RNA.py
cd ../..

After these steps, the Python sdist and wheel packages can be build as usual.

Unofficial Julia Interface

An unofficial interface of the ViennaRNA Package for the Julia Programming Language exists at JuliaHub.