<commit_before># GWAS_Analysis_Pipeline

## Overview and Purpose
------------------------
An automated pipeline to analyze GWAS data after initial round of QC/filtering has been performed.

<p align="center">
<img src="https://github.com/tbrunetti/GWAS_Analysis_Pipeline/blob/master/how_to_run_flowchat.png" />
</p>


## Software Requirements
------------------------
The following are the minimum software requirements:
* Python version 2.7 (https://www.python.org/)
* R version 3.2 or better (https://cran.r-project.org/)
* PLINK version 1.9 or better (https://www.cog-genomics.org/plink2)
* KING software package (http://people.virginia.edu/~wc9c/KING/manual.html)
* chunkypipes (http://chunky-pipes.readthedocs.io/en/stable/getting_started.html)
* virtualenv -- ONLY required if admin rights are not granted (https://virtualenv.pypa.io/en/stable/) 

__*--Software Requirements that can be installed automatically--*__  
The following list of Python libraries are required but the pipeline can automatically install them if pip is available:
  * SciPy stack, in particular the following packages: (https://scipy.org/)
    * pandas
    * numpy
    * matplotlib
  * Statistics (https://pypi.python.org/pypi/statistics)
  * Pillow (https://pypi.python.org/pypi/Pillow/3.4.2)
  * pyFPDF (http://pyfpdf.readthedocs.io/en/latest/index.html)
  * pyPDF2 (https://pypi.python.org/pypi/PyPDF2/1.26.0)


## User Generated File Requirements
-----------------------------------


## Installing and Running Pipeline on HPC or without sudo privileges
---------------------------------------------------------------------
1. Install, Create, Activate Virutal Environment
2. Clone Repository

### Installation, Creation, and Activation of Virtual Environment (installAtion and creation only needs to ever be done once)
------------------------------------------------------------------------------------------------------------------------------
For users running the pipeline on a HPC system or without administrative privileges, a virtual environment must be created in order to utilize the pipeline to its maximum capabilities and efficiency.  The reason being, certain packages and dependencies can be installed using the pipeline to provide the user with an easy-to-use experience.  Many of these packages will install on your system globally, which cannot be done on shared distributed file systems such as HPC or if administrative rights are not granted on the computer you are using.  To bypass this, you will need to create a Python Virtual Environment.  Below are the steps for installing and creating this environment.  NOTE:  THIS ONLY EVER NEEDS TO BE DONE ONE TIME!

1.  Download and Install virtualenv<commit_msg>added minimum input file requirements<commit_after># GWAS_Analysis_Pipeline

## Overview and Purpose
------------------------
An automated pipeline to analyze GWAS data after initial round of QC/filtering has been performed.

<p align="center">
<img src="https://github.com/tbrunetti/GWAS_Analysis_Pipeline/blob/master/how_to_run_flowchat.png" />
</p>


## Software Requirements
------------------------
The following are the minimum software requirements:
* Python version 2.7 (https://www.python.org/)
* R version 3.2 or better (https://cran.r-project.org/)
* PLINK version 1.9 or better (https://www.cog-genomics.org/plink2)
* KING software package (http://people.virginia.edu/~wc9c/KING/manual.html)
* chunkypipes (http://chunky-pipes.readthedocs.io/en/stable/getting_started.html)
* virtualenv -- ONLY required if admin rights are not granted (https://virtualenv.pypa.io/en/stable/) 

__*--Software Requirements that can be installed automatically--*__  
The following list of Python libraries are required but the pipeline can automatically install them if pip is available:
  * SciPy stack, in particular the following packages: (https://scipy.org/)
    * pandas
    * numpy
    * matplotlib
  * Statistics (https://pypi.python.org/pypi/statistics)
  * Pillow (https://pypi.python.org/pypi/Pillow/3.4.2)
  * pyFPDF (http://pyfpdf.readthedocs.io/en/latest/index.html)
  * pyPDF2 (https://pypi.python.org/pypi/PyPDF2/1.26.0)


## User Generated File Requirements
-----------------------------------
There are two files that are minimally required in order to run the pipeline:
* Input PLINK file either in .bed or .ped format
* Populated sample_sheet_template.xlsx  


## Installing and Running Pipeline on HPC or without sudo privileges
---------------------------------------------------------------------
1. Install, Create, Activate Virutal Environment
2. Clone Repository

### Installation, Creation, and Activation of Virtual Environment (installAtion and creation only needs to ever be done once)
------------------------------------------------------------------------------------------------------------------------------
For users running the pipeline on a HPC system or without administrative privileges, a virtual environment must be created in order to utilize the pipeline to its maximum capabilities and efficiency.  The reason being, certain packages and dependencies can be installed using the pipeline to provide the user with an easy-to-use experience.  Many of these packages will install on your system globally, which cannot be done on shared distributed file systems such as HPC or if administrative rights are not granted on the computer you are using.  To bypass this, you will need to create a Python Virtual Environment.  Below are the steps for installing and creating this environment.  NOTE:  THIS ONLY EVER NEEDS TO BE DONE ONE TIME!

1.  Download and Install virtualenv
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