Difference between revisions of "CGATools"

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m (Text replace - "<!--Run-->" to "==System Variables== * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory <!--Run--> ")
 
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|{{#vardefine:url|http://cgatools.sourceforge.net/}}
 
|{{#vardefine:url|http://cgatools.sourceforge.net/}}
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
|{{#vardefine:intel|}} <!-- "11.1" -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4" -->
 
|{{#vardefine:mod|1}} <!--MODULES -->
 
 
|{{#vardefine:exe|}} <!--RUNNING -->
 
|{{#vardefine:exe|}} <!--RUNNING -->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
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<!--VERSIONS-->
 
<!--VERSIONS-->
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
[[Modules|modules documentation]]
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
+
==System Variables==
*{{#var:app}}
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
 
* HPC_CGATOOLS_BIN - executable directory
 
* HPC_CGATOOLS_BIN - executable directory
* HPC_CGATOOLS_INC - includes directory
+
 
* HPC_CGATOOLS_DOC - documentation directory
 
==System Variables==
 
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 
 
<!--Run-->
 
<!--Run-->
 
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY|}}
 
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY|}}

Latest revision as of 16:29, 10 June 2022

Description

cgatools website  

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.

Environment Modules

Run module spider cgatools to find out what environment modules are available for this application.

System Variables

  • HPC_CGATOOLS_DIR - installation directory
  • HPC_CGATOOLS_BIN - executable directory




Citation

If you publish research that uses cgatools you have to cite it as follows: R. Drmanac, et. al. Science 327(5961), 78. [DOI: 10.1126/science.1181498]