Difference between revisions of "Tgicl"

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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
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<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
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* HPC_TGICL_DIR - installation directory
 
 
* HPC_TGICL_BIN - executable directory
 
* HPC_TGICL_BIN - executable directory
* HPC_TGICL_LIB - lib directory
 
 
* HPC_TGICL_CONF - conf directory
 
* HPC_TGICL_CONF - conf directory
  
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<!--Run-->
 
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{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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* To copy the default skeleton configuration file to the working directory:
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cp $HPC_TGICL_CONF/tgicl.cfg .
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* To get a full list of tgicl commands:
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perldoc tgicl
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* Sample run
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tgicl -F sample.fasta  -q sample.qual -c 4
 
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Revision as of 17:44, 13 July 2012

Description

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TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets

This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3

Template:App Location

Available versions

  • 2.1

Running the application using modules

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

Get module information for tgicl:

$module spider tgicl

Load the default application module:

$module load tgicl

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

  • HPC_TGICL_DIR - directory where tgicl is located.
  • HPC_TGICL_BIN - executable directory
  • HPC_TGICL_CONF - conf directory

Note:

By default loading the module for tgicl also loads the latest Perl and CAP3 modules. The main version of cap3 is used for analyses. If you wish to use the cap3 version distributed with tgicl, it is located at $HPC_TGICL_BIN/cap3.tgicl

How To Run

  • To copy the default skeleton configuration file to the working directory:
cp $HPC_TGICL_CONF/tgicl.cfg .
  • To get a full list of tgicl commands:
perldoc tgicl
  • Sample run
tgicl -F sample.fasta  -q sample.qual -c 4