Difference between revisions of "Trinity"

Revision as of 23:55, 30 January 2012

Description

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

Available versions

r20110519
r20110820 (default)

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.

@@ Line 29: / Line 29: @@
 <!--Location-->
 {{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Available versions==
+* r20110519
+* r20110820 (default)
 <!-- -->
 {{#if: {{#var: mod}}|==Using application with environment modules system==
@@ Line 35: / Line 38: @@
 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.