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

@@ Line 2: / Line 2: @@
 __NOEDITSECTION__
 [[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"
--->
 {|
 <!--Main settings - REQUIRED-->
@@ Line 16: / Line 7: @@
 |{{#vardefine:ver|20071015}}
 |{{#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:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 34: / Line 20: @@
 {{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].
+CAP3 is a sequence assembly program.
 Intel processor optimized versions of cap3 and formcon are installed at HPC.
@@ Line 42: / Line 28: @@
 In addition, pcap binaries are also provided.
 <!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
+==Required Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+[[Modules|modules documentation]]
+===Serial===
+*{{#var:app}}
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_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
-{{#if: {{#var: exe}}|==How To Run==
+<!--Additional-->
+{{#if: {{#var: exe}}|==Additional Information==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 53: / Line 44: @@
 {{#if: {{#var: pbs}}|==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)|}}
 {{#if: {{#var: testing}}|==Performance==
@@ Line 63: / Line 54: @@
 WRITE CITATION HERE
 |}}
+=Validation=
+* Validated 4/5/2018

Difference between revisions of "CAP3"