Requirements

• Compiler requirements To compile and install GTfold you will need a C/C++ compiler, autotools, and GMP.
• Parallelization requirements For parallelization, the compiler needs to implement the OpenMP API. (GNU gcc 4.3.2, for example, implements the OpenMP API. See OpenMP Compilers for details.)

More detailed help to fulfill necessary requirements can be found here.

Downloading Source

Download

General users should got to the GTfold github download page and click on "download .tar.gz".

Users interested in checking out the source code from our githup repository should see the Repository section below.

Unzip and unpack

The above command unpacks the GTfold package into a sub-directory gtfold-x where x is the version number.

Installation

GTfold has been tested on Linux, Mac OSX, and Windows (with Cygwin). Once you have downloaded the GTfold source code using one of the above methods, navigate to the gtfold-mfe directory and configure, compile, and install GTfold (either in local or global directories):

• In a local directory
  If you want to install GTfold as non-root user, you can force the configure to install in a local directory.
  ./configure --prefix=LOCAL_DIR
  The above command will try to detect the compiler and try to set the appropriate flags for OpenMP and etc. Make sure that configure completed successfully before moving on to the next step.
  make
  This will compile GTfold using the options detected from configure.
  make install
  This step will install GTfold in LOCAL_DIR/bin where LOCAL_DIR IS the local directory specified in the configure command.
• In global directories (requires root permissions)
  ./configure
  make
  sudo make install
  This step will install GTfold in the global directory if no option is specified to by configure.

Also, you can specify C and C++ compiler using the CC and CXX variables. For example,

(In particular, Mac users with OSX 10.7 may need to do this to ensure the default Mac C/C++ compiler is not used.)

Developer options

Note that developer options only apply to gtboltzmann.

option	description
--checkfraction	Checks that for each structure, the probability used in stochastic sampling matches the probability of that structure according to the Boltzmann Distribution.
--exactintloop	Includes structures with abitrarily many unpaired nucleotides in internal loops. Note: using this option increases the running time by a factor of N, where N is the sequence length.
--parallelsample	Paralellizes the sampling of each individual structure. Only valid in combination with --sample.
--printarrays	Writes partition function arrays to output-prefix.pfarrays.
--sampleenergy DOUBLE	Writes only sampled structures with free energy equal to DOUBLE to file output-prefix.sample. Only valid in combination with --sample.
--separatectfiles [--ctfilesdir DIR] [--summaryfile NAME]	Writes each sampled structure to a separate .ct file in the DIR directory. Also writes a summary of the sampled structures to NAME in DIR. Default directory is the working directory specified with -w, and the default summary file name is stochaSampleSumary.txt Only valid in combination with --sample.

Repository

The GTfold code repository is publicly hosted on GitHub. Users can access the source code for free with no account required. Or for code contributions, please fork the repository and send a pull request.

Accessing the source code requires a git client. If your system doesn't already have git installed (check by typing "git --version" into a terminal), then download git.

Download a copy of the source with the following command:

Reporting Bugs

We have different trackers enabled for our project. Users can report bugs, request for new features, place support requests et. at the following tracker page.

Support

• We have different trackers enabled for our project. Users can report bugs, request for new features, place support requests et. at the following tracker page.
• You can email the GTfold administrators for any unresolved issues with GTfold

Last updated: August 29, 2012