Difference between revisions of "CAP3"

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m (Text replace - "Usage policy" to "Usage Policy")
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__NOEDITSECTION__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
 
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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INTEL - Version of the Intel Compiler e.g. "11.1"
 
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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:intel|}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
CAP3 is a sequence assembly program. See documentation at [http://deepc2.psi.iastate.edu/aat/cap/capdoc.html capdoc site].
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CAP3 is a sequence assembly program.
  
 
Intel processor optimized versions of cap3 and formcon are installed at HPC.  
 
Intel processor optimized versions of cap3 and formcon are installed at HPC.  
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In addition, pcap binaries are also provided.
 
In addition, pcap binaries are also provided.
 
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{{#if: {{#var: mod}}|==Execution Environment and Modules==
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==Required Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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[[Modules|modules documentation]]
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===Serial===
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*{{#var:app}}
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==System Variables==
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* 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
 
* HPC_CAP3_DOC - location of the CAP3 docs directory
 
* HPC_CAP3_DOC - location of the CAP3 docs directory
 
* HPC_CAP3_EXAMPLE - location of the CAP3 examples directory
 
* HPC_CAP3_EXAMPLE - location of the CAP3 examples directory
{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: exe}}|==Additional Information==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
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{{#if: {{#var: conf}}|==Configuration==
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WRITE CITATION HERE
 
WRITE CITATION HERE
 
|}}
 
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:02, 6 December 2019

Description

cap3 website  

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.

Required Modules

modules documentation

Serial

  • cap3

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




Validation

  • Validated 4/5/2018