Difference between revisions of "CGATools"

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Revision as of 18:31, 16 May 2012


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The Complete Genomics Analysis Tools (cgatools) is an open source project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities, but a C++ API is available as well. The general areas of functionality include genome comparison, format conversion, and reference tools. Template:App Location

Available versions


Running the application using modules

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

Get module information for cgatools:

$module spider cgatools

Load the default application module:

$module load cgatools

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

  • HPC_CGATOOLS_DIR - directory where cgatools is located.
  • HPC_CGATOOLS_BIN - executable directory
  • HPC_CGATOOLS_INC - includes directory
  • HPC_CGATOOLS_DOC - documentation directory