RNAstructure.md

+# RNAstructure
+
+## Installation
+**Prerequisites**
+* Follow the instructions in the [Quickstart](Quickstart).
+* Ensure you have the programs required to build the software.
+
+First, in the terminal, navigate to the directory where you want to copy the source code.  Afterwards, you should be able to copy the source code  using the following command.
+
+```Bash
+git clone ssh://git@rna.urmc.rochester.edu:26/mathews-lab/RNAstructure.git
+```
+
+If this does not work, have one of the GitLab administrators (David Mathews, Richard Watson, or Jeffrey Zuber) verify that your user account is a member of the mathews-lab user group.  You can then compile the software using the following commands:
+
+```Bash
+cd RNAstructure
+make all
+```
+
+## Running Programs
+
+After compilation, the program executables will be in the _exe_ directory within the RNAstructure folder.  You should ensure that the executables are available in the PATH environment variable.  To add a directory to the PATH environment variable, edit the _.profile_ file in your home directory with the following line:
+
+```
+PATH=your_directory_path:$PATH
+```
+
+Before running any programs from RNAstructure, you should first define the DATAPATH environment variable, which tells RNAstructure where to find the thermodynamic parameter files.  These parameter files can be found in the _datatables_ folder in the RNAstructure source code directory.  This can be done in the command line with the following command:
+
+```
+export DATAPATH=path_to_data_tables
+```
+
+Note that this command needs to be run for every shell session.  To eliminate this requirement, edit the _.profile_ file in your home directory with the following line:
+
+```
+DATAPATH=path_to_data_tables
+```