Difference between revisions of "CGATools"

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m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
m (Text replacement - "#uppercase" to "uc")
 
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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-->
==Available versions==
+
<!--Modules-->
* 1.5.0.31
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==Required Modules==
<!-- -->
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[[Modules|modules documentation]]
{{#if: {{#var: mod}}|==Running the application using modules==
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===Serial===
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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*{{#var:app}}
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_CGATOOLS_BIN - executable directory
 
* HPC_CGATOOLS_BIN - executable directory
* HPC_CGATOOLS_INC - includes directory
+
 
* HPC_CGATOOLS_DOC - documentation directory
 
 
<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
<!--Performance-->
 
<!--Performance-->
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:19, 6 December 2019

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.

Required Modules

modules documentation

Serial

  • cgatools

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]


Validation

  • Validated 4/5/2018