Difference between revisions of "CGATools"
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Moskalenko (talk | contribs) m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|cgatools}} | |{{#vardefine:app|cgatools}} | ||
|{{#vardefine:url|http://cgatools.sourceforge.net/}} | |{{#vardefine:url|http://cgatools.sourceforge.net/}} | ||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
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|{{#vardefine:exe|}} <!--RUNNING --> | |{{#vardefine:exe|}} <!--RUNNING --> | ||
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
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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. | 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. | ||
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<!--VERSIONS--> | <!--VERSIONS--> | ||
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| − | <!-- --> | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
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* HPC_CGATOOLS_BIN - executable directory | * HPC_CGATOOLS_BIN - executable directory | ||
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<!--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 | + | {{#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--> | ||
Latest revision as of 13:26, 15 August 2022
Description
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]