Table of Contents

• Description
• General Installation
• Pipeline CLUMPAK(StrAuto) + distruct
  • Requirements
  • Usage
  • Download CLUMPAK
  • Run Main Pipeline (CLUMPAK)
  • Run Distruct for many Ks
• Pipeline Structure_threader
  • Installation
  • Usage
    • Create a "popfile"
    • Edit the "mainparams" and optionally the "extraparams" file
    • Run analysis
    • Plot results
• Pipeline fastSTRUCTURE with Docker
  • Installation
  • Run image under Windows MSYS2 or WSL
  • Run image under Linux/OSX

Description

This repository contains three pipelines with scripts to run locally several types of STRUCTURE analysis :

• Pipeline CLUMPAK analysis of STRUCTURE results produced by StrAuto and generate distruct figures.
• Pipeline Structure_threader with fastStructure
• Pipeline fastStructure with Docker

General Installation

git clone https://github.com/hernanmd/STRUCTUREPipelines.git
cd runstructure

Pipeline CLUMPAK(StrAuto) + distruct

Requirements

• STRUCTURE input file (.str).
  • The default name used in the configuration files is project_data.str
• StrAuto results should be already available in a .zip file
  • The results should be zipped into a single .zip file.
  • Default name is stresults.zip, with the following structure:

       k1.zip
               k1/
			project_data_k1_run10_f
			project_data_k2_run1_f
			...
       k2.zip
               k2/
                       project_data_k1_run10_f
                       project_data_k2_run1_f
			...

Usage

• Put your StrAuto results into a subdirectory
• Edit environment variables in the file rsEnvVars.sh

Download CLUMPAK

./rsGetClumpak.sh

Run Main Pipeline (CLUMPAK)

• The runStrClumpak script performs the following actions:
  • Read environment variables in rsEnvVars.sh as parameters.
  • Create the output directory.
  • Build the populations file.
  • Run the CLUMPAK Perl script

./runStrClumpak

Run Distruct for many Ks

• The following script perform the following actions:
  • Read environment variables as parameters.
  • Create the output directory.
  • Build the populations file.
  • Run DistructForManyKs perl script

./runStrDistructForManyKs

Pipeline Structure_threader

Installation

WiP

Usage

To use this pipeline you should have your input files both in PED/MAP format (to generate the populations file) and in BED/BIM/FAM format (required by fastSTRUCTURE). ALSO the structure input file, which could be generated from PLINK using the "--recode structure" option. It is highly recommended to put the input files in a separate subdirectory. The output directory will be created if not already present.

Create a "popfile"

# Create the required popfile from the PED file. 
# The first parameter should be a PED file name which should be specified WITHOUT the .ped extension
# The second parameter should be the species name (as understood by PLINK): cow, horse, etc.
# The output is a new file named "popfile" suitable for Structure_threader plots
./mkPopFile ../STRUCTURE_PIPrun/project_input/file species

Edit the "mainparams" and optionally the "extraparams" file

• If you have not mainparams and extraparams files in your input directory, then run the ./runFsStrThreader.sh script to generate a template version of both files.
• Edit with your favorite editor: nano project_input/mainparams

Run analysis

To run Structure_threader you must specify the following parameters

• 1st parameter is the DIRECTORY where input files are located
• 2nd parameter is the BED file (using PED is not valid for now)
• 3rd parameter is the DIRECTORY where output will be written
• 4th parameter is the name of the popfile generated with mkPopFile script.
• 5th parameter is the number of maximum K:

Example:

 ./runFsStrThreader.sh project_input/ file.bed project_output/ popfile 24

The Structure_threader already generates a plots subdirectory with HTML/SVG paired files into the output directory, however this script will also generate a "Comparative Plots" in a comparativePlotAllKs directory

Pipeline fastSTRUCTURE with Docker

Installation

Install Docker Under Windows: Launch MSYS2 Under Linux/OSX: Launch Terminal Fetch fastStructure docker image from https://hub.docker.com/r/dockerbiotools/faststructure

docker pull dockerbiotools/faststructure

Run image under Windows MSYS2 or WSL

# Get the image id from the following command
docker images
# Make a directory for your dataset
mkdir data # Or whatever your population name is
# Install the winpty package if necessary
# pacman -Ss winpty (or apt get winpty)
# Run the image
winpty docker run -it -v /${PWD}/data/:/fastStructure/data 6ca

Run image under Linux/OSX

# Get the image id from the following command
docker images
# Run the image
docker run -it -v /${PWD}/data/:/fastStructure/data 6ca