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After downloading the software to a Linux server, simply type
in the base installation directory. This should build Inchworm and Chrysalis, both written in C++. A version of gcc greater than 4.3 is required. Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software, but Java-1.8 (or higher) is required.
Afterwards, you may want to build the additional plugin components that provide support for downstream analyses in which case you would then type:
Additional tools required for running Trinity include:
Trinity has been tested and is supported on Linux.
To test your installation of Trinity, try assembling the small sample data set provided with Trinity like so:
cd sample_data/test_Trinity_Assembly/ ./runMe.sh