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Releases: magosil86/witsGWAS

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witsGWAS version 0.1.0 (2015-09-01) -- "Mangosteen"

witsGWAS version 0.1.0 (2015-09-01) -- "Mangosteen" Pre-release
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@magosil86 magosil86 released this 19 Nov 13:29
v0.1.0
132cffd
Release Notes

Initial release of witsGWAS.

A python pipeline for Human GWAS analysis that accommodates both Affymetrix (raw .CEL files) and Illumina (Plink binaries) data.

Installation

First step:

WITS Cluster users:

Download the witsGWAS folder to your home directory ensuring that
all the symbolic links between the scripts sub-directory and the witsGWAS
directory are preserved.

linux command: cp -av
Replacing symbolic links: ln -sf /path/to/witsGWAS/scripts/* /path/to/witsGWAS/

Independent users:

Download the witsGWAS folder to your home directory and create symbolic links between all
the scripts in the scripts sub-directory and the witsGWAS directory.

Create witsGWAS folder: mkdir witsGWAS and cd witsGWAS
Extracting the archive: cat witsGWAS-0.1.0.tar.gz.a* | tar xzv
Replacing symbolic links: ln -sf /path/to/witsGWAS/scripts/* /path/to/witsGWAS/

Second step: Edit witsGWAS_SCRIPTS_ROOT_DIR = "/home/lerato/witsGWAS/" in

  1. pipeline_qcaffymetrix.py
  2. pipeline_qcplink_tasks1-5of20.py
  3. pipeline_qcplink_tasks6-14of20.py
  4. pipeline_qcplink_tasks15-20of20.py
  5. pipeline_qcplink_tasks15-20of20_extended.py
  6. pipeline_assoc_testing.py
  7. pipeline_advanced_assoc_testing.py

with the path to your own witsGWAS directory.

Tutorial and Manuals

Visit the wiki at:
https://github.com/magosil86/witsGWAS/wiki

Rights

Copyright (c) 2015 Lerato E. Magosi and Scott Hazelhurst, Sydney Brenner Institute

witsGWAS is free software and is available WITHOUT WARRANTY OF ANY KIND.
You are welcome to redistribute it adhering to the conditions of the MIT license.

Note:

All four parts of the codebase witsGWAS-0.1.0.tar.gz.aa - witsGWAS-0.1.0.tar.gz.ad should be downloaded

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