Difference between revisions of "CAP3"

From UFRC
Jump to navigation Jump to search
m (moved Cap3 to CAP3: correct case)
 
(16 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]]
+
[[Category:Software]][[Category:Biology]][[Category:Assembly]]
<!-- ########  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"
 
-->
 
 
{|
 
{|
 
<!--Main settings - REQUIRED-->
 
<!--Main settings - REQUIRED-->
Line 16: Line 7:
 
|{{#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-->
Line 32: Line 18:
 
<!--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. See documentation at [http://deepc2.psi.iastate.edu/aat/cap/capdoc.html capdoc site].
+
 
<!--Location-->
+
CAP3 is a sequence assembly program.
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+
 
 
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.
<!-- -->
+
 
{{#if: {{#var: mod}}|==Running the application using modules==
+
In addition, pcap binaries are also provided.
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
<!--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}}|==How To Run==
+
* 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==
Line 49: Line 42:
 
{{#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==
+
{{#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