Difference between revisions of "DDocent"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|ddocent}} | |{{#vardefine:app|ddocent}} | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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| − | < | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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e.g. for a single core with 2Gb RAM for 10 minutes: | e.g. for a single core with 2Gb RAM for 10 minutes: | ||
| − | srun -p | + | srun -p hpg-dev --pty -u bash -i |
Alternatively, load the ‘ufrc’ module and execute ‘srundev’. | Alternatively, load the ‘ufrc’ module and execute ‘srundev’. | ||
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To get 8 cores and 6gb RAM per core for 1 hour run: | To get 8 cores and 6gb RAM per core for 1 hour run: | ||
| − | srun -p | + | srun -p hpg-dev -n 8 -mem-per-cpu 6 -t 60:00 -pty -u bash -i |
|}} | |}} | ||
Latest revision as of 14:29, 15 August 2022
Description
This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD data. It is designed to run on Linux based machines with large memory capacity and multiple processing cores.
Environment Modules
Run module spider ddocent to find out what environment modules are available for this application.
System Variables
- HPC_DDOCENT_DIR - installation directory
Additional Information
This module will only work within an interactive job.
e.g. for a single core with 2Gb RAM for 10 minutes:
srun -p hpg-dev --pty -u bash -i
Alternatively, load the ‘ufrc’ module and execute ‘srundev’.
To get 8 cores and 6gb RAM per core for 1 hour run:
srun -p hpg-dev -n 8 -mem-per-cpu 6 -t 60:00 -pty -u bash -i