Installation

Biers requires MATLAB installation. Unlike HiTRACE, it has no restrictions on versions.

To install Biers, simply:

• From GitHub, download the zip or tar file of the repository and unpack; or

git clone https://github.com/ribokit/Biers.git

• In MATLAB, go to “Set Path”. Then “Add with Subfolders” of the target path/to/Biers/Scripts/.

• Make sure you have set in your environment the variables DATAPATH (for RNAstructure) and VARNA (for VARNA). If you are on a Mac or Linux, put lines like the following in your .bash_profile:

export DATAPATH=$HOME/src/RNAstructure/data_tables/
export VARNA=$HOME/src/VARNA.jar

See also the Biers Dependencies page.

• Makes sure that you start MATLAB from terminal, as follows.

In order to get Biers running with RNAstructure in MATLAB, you have to launch MATLAB from terminal every time.

This is due to the inheritance of DATAPATH environment variable. To launch MATLAB from terminal, run:

/Applications/MATLAB_R20XXa.app/bin/matlab

Replace your MATLAB version in the command.

We recommend creating an alias to save us some time in the future. Edit the ~/.bash_profile, add a line:

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

Again, restart your terminal to take effect. Now you only need to type matlab to launch MATLAB!

A complete guide on the whole setup, including gcc, RNAstructure, VARNA, is described at the Biers dependencies page.

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