Trinity: Difference between revisions

Revision as of 16:45, 14 October 2011

Description

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Trinity contains three applications - Inchworm, Chrysalis, and Butterfly. Template:App Location

Using application with environment modules system

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

Get module information for trinity:

$module spider trinity

Load the default application module:

$module load trinity

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

HPC_TRINITY_DIR - directory where trinity is located.

How To Run

To run Trinity after you load the module use the "Trinity.pl" perl script, or run_Trinity.sh shell script, which is particularly useful if the optional ALLPATHS-LG software is enabled.

Installation

Trinity is meant to be installed "in-tree". To install, just download Trinity, open the archive, and type 'make'. Optional software ALLPATHS-LG - a WGS (Whole Genome Shotgun) assembler can be used with trinity if available and the ALLPATHSLG_BASEDIR environment variable is set. Currently, we do not provide ALLPATHS-LG at the UF HPC.

@@ Line 20: / Line 20: @@
 <!--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:exe|1}} <!--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 ######## -->
@@ Line 36: / Line 30: @@
 {{App_Location|app={{#var:app}}|{{#var:ver}}}}
 <!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
+{{#if: {{#var: mod}}|==Using application with environment modules system==
 {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
-{{#if: {{#var: exe}}|==Manual execution instructions==
+{{#if: {{#var: exe}}|==How To Run==
-WRITE INSTRUCTIONS ON RUNNING THE APP WITHOUT MODULES HERE|}}
+To run Trinity after you load the module use the "Trinity.pl" perl script, or run_Trinity.sh shell script, which is particularly useful if the optional ALLPATHS-LG software is enabled.
-{{#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
 |}}
 ==Installation==
 Trinity is meant to be installed "in-tree".  To install, just download Trinity, open the archive, and type 'make'. Optional software ALLPATHS-LG - a WGS (Whole Genome Shotgun) assembler can be used with trinity if available and the ALLPATHSLG_BASEDIR environment variable is set. Currently, we do not provide ALLPATHS-LG at the UF HPC.