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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.
Note, starting with Trinity-v2.8, cmake is required for building the software.
Afterwards, you may want to build the additional plugin components that provide support for downstream analyses in which case you would then type:
% make plugins
Additional tools required for running Trinity include:
If you want to install Trinity in a central location (not required), you can
% make install
and it'll copy the software package to /usr/local/bin/trinityrnaseq-version
You can set the environmental variable TRINITY_HOME to point to this, which will make it easy to access both Trinity as well as supported downstream applications that come bundled with Trinity.
% export TRINITY_HOME=/path/to/trinity/installation/dir
You can put the above command in your ~/.bashrc file so it'll be available to you by default.
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