Difference between revisions of "CAP3"
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:Assembly]] |
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<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
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|{{#vardefine:ver|20071015}} | |{{#vardefine:ver|20071015}} | ||
|{{#vardefine:url|http://seq.cs.iastate.edu/}} | |{{#vardefine:url|http://seq.cs.iastate.edu/}} | ||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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<!--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}}}}|}} |
| − | CAP3 is a sequence assembly program | + | |
| − | + | CAP3 is a sequence assembly program. | |
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Intel processor optimized versions of cap3 and formcon are installed at HPC. | Intel processor optimized versions of cap3 and formcon are installed at HPC. | ||
Opteron optimized versions of these binaries are named cap3-opteron and formcon-opteron. | Opteron optimized versions of these binaries are named cap3-opteron and formcon-opteron. | ||
| − | <!-- --> | + | |
| − | + | In addition, pcap binaries are also provided. | |
| − | + | <!--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 | ||
* HPC_CAP3_BIN - location of the CAP3 executables directory | * HPC_CAP3_BIN - location of the CAP3 executables directory | ||
| − | {{#if: {{#var: exe}}|== | + | * HPC_CAP3_DOC - location of the CAP3 docs directory |
| + | * HPC_CAP3_EXAMPLE - location of the CAP3 examples directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#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)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 13:19, 15 August 2022
Description
CAP3 is a sequence assembly program.
Intel processor optimized versions of cap3 and formcon are installed at HPC.
Opteron optimized versions of these binaries are named cap3-opteron and formcon-opteron.
In addition, pcap binaries are also provided.
Environment Modules
Run module spider cap3 to find out what environment modules are available for this application.
System Variables
- HPC_CAP3_DIR - installation directory
- HPC_CAP3_BIN - location of the CAP3 executables directory
- HPC_CAP3_DOC - location of the CAP3 docs directory
- HPC_CAP3_EXAMPLE - location of the CAP3 examples directory