Difference between revisions of "CAP3"

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m (Text replacement - "#uppercase" to "uc")
 
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__NOTOC__
 
__NOTOC__
 
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[[Category:Software]]
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
<!-- ########  Template Configuration ######## -->
 
<!--Edit definitions of the variables used in template calls
 
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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{|
 
{|
 
<!--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/}}
<!--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-->
 
|{{#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}}}}|}}
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{{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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<!--Location-->
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CAP3 is a sequence assembly program.
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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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.
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In addition, pcap binaries are also provided.
 
<!-- -->
 
<!-- -->
{{#if: {{#var: mod}}|==Running the application using 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
{{#if: {{#var: exe}}|==How To Run==
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* HPC_CAP3_DOC - location of the CAP3 docs directory
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* HPC_CAP3_EXAMPLE - location of the CAP3 examples directory
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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==
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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