Difference between revisions of "Trinity"
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The former tests the whole flow, and the latter tests Butterfly only. | The former tests the whole flow, and the latter tests Butterfly only. | ||
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| + | __NOTOC__ | ||
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]] | ||
| + | <!-- ######## Template Configuration ######## --> | ||
| + | <!--Edit definitions of the variables used in template calls | ||
| + | Required variables: | ||
| + | app - lowercase name of the application e.g. "amber" | ||
| + | url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/" | ||
| + | Optional variables: | ||
| + | INTEL - Version of the Intel Compiler e.g. "11.1" | ||
| + | MPI - MPI Implementation and version e.g. "openmpi/1.3.4" | ||
| + | --> | ||
| + | {| | ||
| + | <!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|test}} | ||
| + | |{{#vardefine:url|http://sourceforge.net}} | ||
| + | <!--Compiler and MPI settings - OPTIONAL --> | ||
| + | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
| + | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | ||
| + | <!--Choose sections to enable - OPTIONAL--> | ||
| + | |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | ||
| + | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
| + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
| + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| + | PASTE OR ENTER EXTENDED DESCRIPTION HERE OR REMOVE THIS LINE | ||
| + | [PASTE A LINK TO UPSTREAM DOCS OR REMOVE THIS LINE Upstream documentation] for {{#var:app}}. | ||
| + | <!--Location--> | ||
| + | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| + | ADD EXECUTABLE AND LIBRARY LOCATION DETAILS FOR INSTALLED VERSIONS OR REMOVE THIS MESSAGE | ||
| + | <!-- --> | ||
| + | {{#if: {{#var: mod}}|==Running the application using modules== | ||
| + | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| + | {{#if: {{#var: exe}}|==Manual execution instructions== | ||
| + | WRITE INSTRUCTIONS ON RUNNING THE APP WITHOUT MODULES HERE|}} | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | {{#if: {{#var: policy}}|==Usage policy== | ||
| + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
| + | {{#if: {{#var: testing}}|==Performance== | ||
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| + | WRITE CITATION HERE | ||
| + | |}} | ||
Revision as of 16:21, 14 October 2011
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
{{{name}}} website
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.