Difference between revisions of "DDocent"
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(Created page with "Category:SoftwareCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ddocent}} |{{#vardefine:url|https://github.com/jpuritz/dDocent}} <!--CONFIGURATION...") |
Moskalenko (talk | contribs) m (Text replacement - "hpg2-dev" to "hpg-dev") |
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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:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 | ||
|}} | |}} | ||
Revision as of 14:30, 29 September 2021
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.
Required Modules
Serial
- ddocent
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