Installing Trinity

Installing Trinity

For a complete installation of Trinity, please see the versions and installation instructions in our Dockerfile. Better yet, use our Docker or Singularity images and there's no additional installation required!

If you decide to install Trinity natively and not use the prepackaged images, then:

after downloading the software to a Linux server, simply type

%  make 

in the base installation directory. This should build Inchworm and Chrysalis, both written in C++. 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:

• bowtie2
• jellyfish
• salmon
• samtools

See versions of tools used in our Dockerfile

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.

Additional installation requirements:

• python 2.7 or 3.* with numpy

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