Difference between revisions of "Structure"
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|structure}} | |{{#vardefine:app|structure}} | ||
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You will have to provide the mainparams and extraparams files in a working | You will have to provide the mainparams and extraparams files in a working | ||
directory from which you run the software or via the arguments: | directory from which you run the software or via the arguments: | ||
| − | * -m path/to/mainparams | + | * -m /path/to/mainparams |
| − | * -e path/to/extraparams | + | * -e /path/to/extraparams |
| − | * -s path/to/STRATparams | + | * -s /path/to/STRATparams |
Sample files are located in the''$HPC_STRUCTURE_CONF'' directory. | Sample files are located in the''$HPC_STRUCTURE_CONF'' directory. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_STRUCTURE_BIN - executable directory | * HPC_STRUCTURE_BIN - executable directory | ||
* HPC_STRUCTURE_DOC - documentation directory | * HPC_STRUCTURE_DOC - documentation directory | ||
Latest revision as of 16:03, 22 August 2022
Description
Structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers
You will have to provide the mainparams and extraparams files in a working directory from which you run the software or via the arguments:
- -m /path/to/mainparams
- -e /path/to/extraparams
- -s /path/to/STRATparams
Sample files are located in the$HPC_STRUCTURE_CONF directory.
Environment Modules
Run module spider structure to find out what environment modules are available for this application.
System Variables
- HPC_STRUCTURE_DIR - installation directory
- HPC_STRUCTURE_BIN - executable directory
- HPC_STRUCTURE_DOC - documentation directory
- HPC_STRUCTURE_CONF - directory with sample configuration files