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 :doc:`/configuration` section
  *before* you install our software if you intend to deviate
  from the default setup.

.. toctree::
   :maxdepth: 1
   :caption: Contents:


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 <https://www.tbi.univie.ac.at/RNA/#download>`_
of the official ViennaRNA homepage.

.. admonition:: See also...

  :ref:`install:binary packages`, :ref:`install:using conda`, and :ref:`install:python interface only`

Quick-start
^^^^^^^^^^^

Usually you'll just download the `latest source tarball <https://www.tbi.univie.ac.at/RNA/#source_code_packages>`_,
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 <https://github.com/ViennaRNA/ViennaRNA>`_
hosted at https://github.com:

.. code:: bash

  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``:

.. code:: bash

  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``:

.. code:: bash

  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:

.. code:: bash

  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 <https://www.doxygen.nl/>`_. The extracted API documentation
is then processed further by `breathe <https://breathe.readthedocs.io/>`_ and finally
integrated into a comprehensive reference manual written in
`ReStructuredText <https://docutils.sourceforge.io/rst.html>`_. This manual is then
usually compiled into HTML and PDF format by `Sphinx <https://www.sphinx-doc.org/>`_.

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 :ref:`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.:

.. code:: bash

  ./configure --disable-openmp

.. admonition:: See also...

  :ref:`configuration:openmp`, :ref:`configuration:universal binaries`, and :ref:`faq: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 <https://bioconda.github.io/>`_
channels

.. code:: bash

  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 <http://bioconda.github.io/recipes/viennarna/README.html>`_
through

.. code:: bash

  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 <https://www.tbi.univie.ac.at/RNA/#binary_packages>`_.

Python interface only
---------------------

The Python 3 interface for the ViennaRNA Package library is
`available at PyPI <https://pypi.org/project/ViennaRNA/>`_ 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

.. code:: bash

  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
  :ref:`above <install:Installing from git repository>`. In particular,
  some autogenerated static files that are compiled into RNAlib must
  be generated. To do so, run

  .. code:: bash

    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

  .. code:: bash

    cd doc
    make refman-html
    cd ..

  Finally, the swig wrapper must be build using

  .. code:: bash

    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 <https://julialang.org/>`_ exists at
`JuliaHub <https://juliahub.com/ui/Packages/ViennaRNA/lOl0n/>`_.
