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...") |
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|{{#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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{{#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 hpg2-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 hpg2-dev -n 8 -mem-per-cpu 6 -t 60:00 -pty -u bash -i | ||
| + | or | ||
| + | |||
| + | srundev -n 8 -mem-per-cpu 6 -t 60:00 | ||
| + | Please open support requests for any problems you encounter or for any questions not addressed on our website or wiki. | ||
|}} | |}} | ||
Revision as of 19:25, 23 May 2016
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_{{#uppercase: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 hpg2-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 hpg2-dev -n 8 -mem-per-cpu 6 -t 60:00 -pty -u bash -i or
srundev -n 8 -mem-per-cpu 6 -t 60:00 Please open support requests for any problems you encounter or for any questions not addressed on our website or wiki.