Difference between revisions of "CGATools"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|cgatools}} |{{#vardefine:url|http://cgatools.sourceforge....") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (13 intermediate revisions by 2 users not shown) | |||
| Line 4: | Line 4: | ||
|{{#vardefine:url|http://cgatools.sourceforge.net/}} | |{{#vardefine:url|http://cgatools.sourceforge.net/}} | ||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
| − | |||
| − | |||
| − | |||
|{{#vardefine:exe|}} <!--RUNNING --> | |{{#vardefine:exe|}} <!--RUNNING --> | ||
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
| Line 13: | Line 10: | ||
|{{#vardefine:testing|}} <!--TESTING/PROFILING--> | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 19: | Line 16: | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
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. | ||
| − | + | ||
| − | |||
<!--VERSIONS--> | <!--VERSIONS--> | ||
| − | + | <!--Modules--> | |
| − | + | ==Required Modules== | |
| − | <!-- --> | + | [[Modules|modules documentation]] |
| − | + | ===Serial=== | |
| − | + | *{{#var:app}} | |
| − | + | ==System Variables== | |
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_CGATOOLS_BIN - executable directory | * HPC_CGATOOLS_BIN - executable directory | ||
| − | + | ||
| − | |||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| Line 43: | Line 40: | ||
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--> | ||
| Line 53: | Line 50: | ||
<!--Citation--> | <!--Citation--> | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{ | + | If you publish research that uses {{#var:app}} you have to cite it as follows: |
| − | + | R. Drmanac, et. al. Science 327(5961), 78. [DOI: 10.1126/science.1181498]|}} | |
<!--Installation--> | <!--Installation--> | ||
{{#if: {{#var: installation}}|==Installation== | {{#if: {{#var: installation}}|==Installation== | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:19, 6 December 2019
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.
Required Modules
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