GenPipes Check List

Before you begin using GenPipes for the first time, it would be useful to quickly go over the basic requirements of using GenPipes. This checklist is created to help you get started with GenPipes quickly and get your bearings correct before you embark upon genomic analysis with GenPipes.

Skill sets and domain know-how

The following table lists some of the skill sets, technologies and know-how that a GenPipes user is expected to have.

Requirements

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High Performance Computing (HPC) for genomics - environment and software modules used

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Cluster Computing, Cloud environment for genomics

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Compute Canada HPC infrastructure usage account and familiarity

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Use of shared, distributed File Systems such as CVMFS

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HPC Schedulers such as PBS, Slurm

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Bioinformatics Software Dependencies (Local/Pre-installed on CCDB)

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GenPipes Basic Concepts - Pipelines, steps etc.

Pre-requisites for running GenPipes

Besides the skills and technologies listed above, you need powerful hardware and some pre-installed software modules before you can run GenPipes. For a complete list, please refer to Checklist of Pre-requisites for Running GenPipes for details.