Difference between revisions of "Structure threader"
Johnbullard (talk | contribs) (Created page with "Category:Software Category:Utility Category:Wrapper Category:Structure {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|Structure_threader}} |{{#vardefine:ur...") |
Johnbullard (talk | contribs) (Add info about loading Structure alongside Structure_threader) |
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|1}} <!--JOB SCRIPTS--> | |{{#vardefine:job|1}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | Structure_wrapper provides its own binary for Structure. However, this binary has not been compiled for or tested on HiPerGator. | ||
| − | + | This means that, when using Structure, your job scripts should load the "structure" module in addition to "structure_threader": | |
| − | + | module load structure/2.3.4 | |
| + | module load structure_threader/1.3.10 | ||
| + | and, when you call structure_threader, pass the "-st" flag with the path to the HiPerGator-provided Structure binary (using the <code>${HPC_STRUCTURE_BIN}</code> environment variable from the module: | ||
| + | structure_threader run ... '''-st ${HPC_STRUCTURE_BIN}/structure''' | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Revision as of 12:52, 2 May 2022
Description
A wrapper program to parallelize the runs of Structure, fastStructure, MavericK and ALStructure software.
Environment Modules
Run module spider Structure_threader to find out what environment modules are available for this application.
System Variables
- HPC_STRUCTURE_THREADER_DIR - installation directory
- HPC_STRUCTURE_THREADER_BIN - executable directory
Additional Information
Structure_wrapper provides its own binary for Structure. However, this binary has not been compiled for or tested on HiPerGator.
This means that, when using Structure, your job scripts should load the "structure" module in addition to "structure_threader":
module load structure/2.3.4 module load structure_threader/1.3.10
and, when you call structure_threader, pass the "-st" flag with the path to the HiPerGator-provided Structure binary (using the ${HPC_STRUCTURE_BIN} environment variable from the module:
structure_threader run ... -st ${HPC_STRUCTURE_BIN}/structure
Job Script Examples
See the Structure threader_Job_Scripts page for Structure_threader Job script examples.
Citation
If you publish research that uses Structure_threader you have to cite it as follows:
If you use Structure_threader, please cite our Molecular Ecology Resources paper: http://doi.org/10.1111/1755-0998.12702