Difference between revisions of "CAP3"

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m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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[[Category:Software]][[Category:Biology]][[Category:Assembly]]
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Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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|{{#vardefine:ver|20071015}}
 
|{{#vardefine:ver|20071015}}
 
|{{#vardefine:url|http://seq.cs.iastate.edu/}}
 
|{{#vardefine:url|http://seq.cs.iastate.edu/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#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-->
 
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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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<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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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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<!--Additional-->
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{{#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 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)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 13:19, 15 August 2022

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.

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