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3DScape Installation Guide
To use 3DScape , you need to install Cytoscape first. Besides, 3DScape requires VTK libraries to run.
The VTK shared libraries can be obtained here (32-bit Linux, 64-bit Linux).
You can also compile VTK from source code by following this instruction.
There are some dependency libraries should also be installed, take Ubuntu Linux for example, you may need:
libjpeg62_6b1,
libjpeg62-dev_6b1,
libmysqlclient16_5.1.56,
libnetcdf6_4.1.1,
libvtk5.6,
libvtk-java.
The vtkCys libraries are updated along with 3DScape, and can be downloaded here(32-bit Linux, 64-bit Linux).
After download, extract vtk and vtkCys packages to a directory. Keep in mind you need to point $LD_LIBRARY_PATH to that directory, This can be done by add these lines to your .bashrc file, which is located under your home folder
export LD_LIBRARY_PATH=/home/yourusername/VTK:\
/home/yourusername/VTK/jni:$LD_LIBRARY_PATH
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Put vtkCysPlugin.jar into cytoscape/plugins/ folder, the make a bash script like this:
java -Djava.library.path="/home/yourusername/VTK:$LD_LIBRARY_PATH" \
-Xss10M -Xmx1550M -jar cytoscape.jar -p plugins "$@"
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Save and execute the script, the 3DScape will be automatically loaded upon the startup of Cytoscape.
See also 3DScape Online User Manual
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