Difference between revisions of "Trinity"
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
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{| | {| | ||
<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|trinity}} |
| − | |{{#vardefine:url|http://sourceforge.net}} | + | |{{#vardefine:url|http://trinityrnaseq.sourceforge.net/}} |
<!--Compiler and MPI settings - OPTIONAL --> | <!--Compiler and MPI settings - OPTIONAL --> | ||
|{{#vardefine:intel|}} <!-- E.g. "11.1" --> | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| − | + | Trinity contains three applications - Inchworm, Chrysalis, and Butterfly. | |
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<!--Location--> | <!--Location--> | ||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
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<!-- --> | <!-- --> | ||
{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
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WRITE CITATION HERE | 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. | ||
Revision as of 16:26, 14 October 2011
Description
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Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.
Template:App Location
Running the application using modules
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.
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.