Click here to download the latest version (v1.9) of Gene Stacker. Some example input files, among which the one discussed on the example page, are included in the package. Previous versions are also available below.
|v1.9||28 August 2015||Download|
|v1.8||21 January 2015||Download|
|v1.7||06 January 2015||Download|
|v1.6||10 September 2014||Download|
|v1.5||17 March 2014||Download|
|v1.4||06 December 2013||Download|
|v1.3||20 November 2013||Download|
|v1.2||23 September 2013||Download|
|v1.1||20 August 2013||Download|
|v1.0||13 August 2013||Download|
The downloadable package also includes a wrapper script
genestacker.R to run Gene Stacker from R.
See the usage page for instructions on how to use this interface.
The CLI is ready to use and does not require installation, see the usage page for instructions. When
running Gene Stacker for the first time, a config file named
will be created in your home directory under
~/genestacker/. It has the following structure:
# Genestacker config file # Absolute path to the dot command line tool, # # e.g.: # # dot.path=/usr/bin/dot (Linux) # dot.path=/usr/local/bin/dot (Linux) # dot.path=C:/Program Files/Graphviz2.32/bin/dot.exe (Windows) # dot.path=C:\\Program Files\\Graphviz2.32\\bin\\dot.exe (Windows) dot.path=/usr/local/bin/dot # location of crossing scheme XML Schema crossingscheme.xml.schema=http://genestacker.ugent.be/xml/crossingscheme.xsd # location of genestacker input XML Schema genestackerinput.xml.schema=http://genestacker.ugent.be/xml/genestacker_input.xsdThis file can be edited using your favorite text editor (on Windows, Notepad may show everything on a single line, use another text editor like WordPad to avoid this). Usually, only the
dot.pathentry should be adjusted to the absolute path of the
dotcommand line tool, which comes with the Graphviz software. For Unix operating systems, after installing Graphviz, open a terminal window and type
$ which dot /usr/local/bin/dotto find out where the
dotcommand has been installed, in our case in
/usr/local/bin/dot. On Windows, the
dot.exeexecutable is located in the
bindirectory of the Graphviz installation folder, which can be specified when installing Graphviz. By default, the path will be
[VERSION]should be replaced with the appropriate version number. Note that in the Gene Stacker config file, you should either use forward slashes or double backslashes as separator in Windows paths, for example
C:/Program Files/Graphviz2.32/bin/dot.exeIf Graphviz is not installed, or if the correct path to the
dotcommand is not set in the config file, Gene Stacker will not produce visualizations of the constructed crossing schedules. Such visualizations can then be generated afterwards based on the output files, see the output section of the usage page for more details.