Difference between revisions of "Structure"
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Moskalenko (talk | contribs) m (Text replace - "==Available versions== (.*)+ <!-- -->" to "<!--Modules-->") |
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|structure}} | |{{#vardefine:app|structure}} | ||
|{{#vardefine:url|http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html}} | |{{#vardefine:url|http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html}} | ||
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|{{#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--> | ||
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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 | + | 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''$HPC_STRUCTURE_CONF'' directory. | ||
<!--Modules--> | <!--Modules--> | ||
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_STRUCTURE_BIN - executable directory | * HPC_STRUCTURE_BIN - executable directory | ||
* HPC_STRUCTURE_DOC - documentation directory | * HPC_STRUCTURE_DOC - documentation directory | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 16:03, 22 August 2022
Description
Structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers
You will have to provide the mainparams and extraparams files in a working directory from which you run the software or via the arguments:
- -m /path/to/mainparams
- -e /path/to/extraparams
- -s /path/to/STRATparams
Sample files are located in the$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