Difference between revisions of "CAP3"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
|||
| (6 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Assembly]] |
{| | {| | ||
<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
| Line 7: | Line 7: | ||
|{{#vardefine:ver|20071015}} | |{{#vardefine:ver|20071015}} | ||
|{{#vardefine:url|http://seq.cs.iastate.edu/}} | |{{#vardefine:url|http://seq.cs.iastate.edu/}} | ||
| − | |||
| − | |||
| − | |||
|{{#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 23: | Line 20: | ||
{{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 | + | 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. | ||
| Line 30: | Line 27: | ||
In addition, pcap binaries are also provided. | In addition, pcap binaries are also provided. | ||
| − | <!-- --> | + | <!--Modules--> |
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * 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}}|== | + | <!--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== | ||
Latest revision as of 13:19, 15 August 2022
Description
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