Difference between revisions of "CAP3"
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] |
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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. | ||
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{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
* 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_EXAMPLE - location of the CAP3 examples directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 16:47, 5 July 2012
Description
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CAP3 is a sequence assembly program. See documentation at capdoc site.
Template:App Location
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.
Running the application using modules
To use cap3 with the environment modules system at HPC the following commands are available:
Get module information for cap3:
$module spider cap3
Load the default application module:
$module load cap3
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CAP3_DIR - directory where cap3 is located.
- 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