Installation — ViennaRNA Package

# 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-2.7.2.tar.gz
    cd ViennaRNA-2.7.2
    ./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-3.35.tar.gz -C src

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

    tar -xjf src/dlib-20.0.tar.bz2 -C src

3. Install the autotools toolchain and the additional maintainer tools `gengetopt`, `help2man`, `flex`, `xxd`, and `swig` if necessary. For instance, in Debian based distributions, the following packages need to be installed:

   > - `build-essential` (basic build tools, such as compiler, linker, etc.)

   > - `autoconf`, `automake`, `libtool`, `pkg-config` (autotools toolchain)

   > - `gengetopt` (to generate command line parameter parsers)

   > - `help2man` (to generate the man pages)

   > - `bison` and `flex` (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. `gfortran` (for `RNAxplorer`)

4. 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.