Difference between revisions of "Parabricks"
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and | + | Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements. |
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| + | Parabricks makes both [https://www.nvidia.com/en-us/docs/parabricks/quickstart-guide/software-overview/pipelines-overview/ Pipelines] and some [https://www.nvidia.com/en-us/docs/parabricks/quickstart-guide/software-overview/standalone-tools-overview/ standalone tools] available. | ||
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srun -p gpu --constraint=rtx6000 -N 1 --cpus-per-task=16 --gpus=1 --mem=32gb --time=200:00 --pty bash -i | srun -p gpu --constraint=rtx6000 -N 1 --cpus-per-task=16 --gpus=1 --mem=32gb --time=200:00 --pty bash -i | ||
| − | It is recommended to use the RTX6000 GPUs because the RTX 2080ti cards do no have enough memory. The '--num-gpus 1' pbrun argument must match the number of requested GPUs. If not specified parabricks will try to run on all | + | It is recommended to use the RTX6000 GPUs because the RTX 2080ti cards do no have enough memory. The '--num-gpus 1' pbrun argument must match the number of requested GPUs. If not specified parabricks will try to run on all gpus on the compute node and exit with an error. |
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Revision as of 16:18, 15 October 2020
Description
Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements.
Parabricks makes both Pipelines and some standalone tools available.
Environment Modules
Run module spider parabricks to find out what environment modules are available for this application.
System Variables
- HPC_PARABRICKS_DIR - installation directory
- HPC_PARABRICKS_BIN - executable directory
Additional Information
An example job resource request based on the Nvidia recommendation:
srun -p gpu --constraint=rtx6000 -N 1 --cpus-per-task=16 --gpus=1 --mem=32gb --time=200:00 --pty bash -i
It is recommended to use the RTX6000 GPUs because the RTX 2080ti cards do no have enough memory. The '--num-gpus 1' pbrun argument must match the number of requested GPUs. If not specified parabricks will try to run on all gpus on the compute node and exit with an error.