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Computational requirements for running the H3ABioNet GWAS workflows. - Lecture 1 H3ABioNet 2018 GWAS Lecture series

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posted on 11.09.2018 by Scott Hazelhurst, Shaun Aron, Sumir Panji, Nicola J. Mulder

Computational requirements for running the H3ABioNet GWAS workflows

The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics:
1. Installing and using Nextflow
2. Installing and using Github
3. Use of containers for packaging and running tools
4. Pulling the GWAS pipeline from Github and running it

As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements:
1. Either a Linux machine or an Apple running macOS
2. Ideally you should have machine with at least 2-4 cores and 8GB of RAM.
3. Java 8
4. Nextflow installed (see installation instructions at https://www.nextflow.io/)
5. Python 3

Please also install either Docker OR the following dependencies using pip3:
Pandas, Matplotlib, Openpyxl, SciPy, NumPy
PLINK 1.9

[Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]:
https://github.com/h3abionet/h3agwas/blob/master/README.md

Funding

Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U24HG006941. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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