Trinity

Trinity is an application for de novo reconstruction of transcriptomes from RNA-Seq data. Its home page is at http://trinityrnaseq.sourceforge.net/.

Installation

Trinity contains three applications - Inchworm, Chrysalis, and Butterfly. They are meant to be installed "in-tree". To install, just download Trinity from their website, untar it, and type 'make'.

Testing

There are two tests which come with Trinity:

/apps/trinity/r20110519/sample_data/runMe.sh
/apps/trinity/r20110519/Butterfly/src/runExample.sh

The former tests the whole flow, and the latter tests Butterfly only.

Description

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PASTE OR ENTER EXTENDED DESCRIPTION HERE OR REMOVE THIS LINE [PASTE A LINK TO UPSTREAM DOCS OR REMOVE THIS LINE Upstream documentation] for test. Template:App Location ADD EXECUTABLE AND LIBRARY LOCATION DETAILS FOR INSTALLED VERSIONS OR REMOVE THIS MESSAGE

Running the application using modules

To use test with the environment modules system at HPC the following commands are available:

Get module information for trinity:

$module spider test

Load the default application module:

$module load test

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_TEST_DIR - directory where test is located.