Rosetta compilation and installation
====================================

``rna_predict`` relies on a few modifications of the Rosetta source code to
work.

Get Rosetta
--------------

Download Rosetta from the official website. The latest set of patches targets
build ``2015wk19`` so it's advised to get a fairly recent weekly build.

Apply patches
----------------

The needed patches are included in the ``contrib/rosetta_patches`` directory.

To apply them ``cd`` to the unpacked Rosetta source and run::

    patch -p1 < /path/to/patches/*.patch

If they don't apply cleanly, for example when targeting a newer version of
Rosetta, they need to be applied manually. The changes are only minor so it
should be possible to do without much effort.

Build and install
--------------------

Build Rosetta normally according the official documentation.

``PATH`` setup
-----------------

``rna_predict`` needs to find the Rosetta binaries as well as some of the helper
scripts from the ``tools`` package.

Also, ``rna_predict`` does not specify the ``-database`` parameter when invoking
Rosetta commands, so the database needs to reside in the default location
or the ``ROSETTA3_DB`` environment variable needs to be set correctly.

The following lines in ``.bashrc`` or similar should be sufficient to make
everything work::

    export ROSETTA3_DB=/path/to/rosetta_database
    export RNA_TOOLS=/path/to/rosetta_tools/rna_tools
    export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS/bin/
    export PATH=$PATH:/path/to/rosetta_source/bin:$RNA_TOOLS/bin