RiboKit : Biers

Basic Inference Engine for RNA Structure

Biers Dependency

This guide has been tested for Mac OS X systems only. We have not used Windows machines for Biers before.

Setting up MATLAB

You may need to launch MATLAB from command-line to make sure it finds all the paths for RNAstructure and VARNA, as outlined below.

Simply double-clicking on the MATLAB icon may not work!

Go into the .bash_profile in your home directory, and include a line like:

alias matlab=/Applications/MATLAB_R20XXa.app/bin/matlab

Use any text editor you prefer, e.g. vim, nano (easiest), emacs.

Make sure you replace the version number (20xxa) with your ‘real’ version number!

RNAstructure

We are using the Command Line (Text Interface) of RNAstructure. Following are instructions that are based on RNAstructure’s help page.

You may already have this compiler or (on Mac OS X) the clang compiler which replaced it; at your terminal type:

which gcc

If you don’t get a path, you can install gcc. One way to do it is through Developer Tools, available for free at the Apple Store.

Alternatively, you can install gcc via brew, a handy package manager for Mac OS X. If you don’t have brew installed, do:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" # may need sudo

Then install gcc with:

brew tap homebrew/versions
brew install gcc49

We have only tested gcc version 4.x. Newer version (e.g. 5.x, 6.x) may have issues with compiler flags. We have also tested clang, which is actually what runs instead of gcc on Max OS X.

Test if gcc is the default C compiler. You can say:

which gcc
gcc --version

If you’re trying to avoid using clang (system default) and instead really want to run this gcc, you may need to get rid of clang, which occupies the namespace. To fix it, try:

brew unlink gcc49
brew link gcc49

Usually, the brew installed gcc exeutables are located at a path like /usr/local/Cellar/gcc/4.x.x/bin (also a copy of each right at /usr/local/bin). Look for gcc-4.x, g++-4.x, c++-4.x, cpp-4.x.


Check /path/to/RNAstructure/compiler.h to make sure CXX=g++ or CXX = g++-4.x.

Now run the following command to compile the code:

cd /path/to/RNAstructure/
make clean
cd RNA_class/
make clean
cd ..
make all
make install # may need sudo make install

Edit file ~/.bash_profile, add a line:

export PATH=/usr/local/bin:$PATH
export DATAPATH=/path/to/RNAstructure/data_tables/

Use any text editor you prefer, e.g. vim, nano (easiest), emacs.

Make sure you replace the path with your ‘real’ path!

Now close the terminal window and start a new one. (This allows the ~/.bash_profile to take effect.)


VARNA

Any of the types listed on the download page works. The minimal Binaries suffices.

Double-click on VARNA.jar

VARNA.jar may ask you to install Java runtime – just follow the instructions. If you see blank data or do not see chemical mapping data, install the latest JDK: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Note: we used to recommend running VARNA through a Web browser, but we are not aware of any browsers that still allow Java applications to run.

export VARNA=/path/to/VARNA.jar

Use any text editor you prefer, e.g. vim, nano (easiest), emacs.

Make sure you replace the path with your ‘real’ path!

Now close the terminal window and start a new one. (This allows the ~/.bash_profile to take effect.)


Summary of what should be in your .bash_profile

After all the installation, check that your home directory’s .bash_profile should have four lines like the following.

export PATH=/usr/local/bin:$PATH
export DATAPATH=/path/to/RNAstructure/data_tables/
export VARNA=/path/to/VARNA.jar
alias matlab=/Applications/MATLAB_R20XXa.app/bin/matlab

Early versions of Biers recommended that these lines be placed in .bashrc. If you are using .bashrc, make sure your .bash_profile has a line like source ~/.bashrc

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