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https://github.com/hernanmd/structurepipelines
Pipelines to run STRUCTURE using multiple front-ends (CLUMPAK+StrAuto, Structure_threader)
https://github.com/hernanmd/structurepipelines
bioinformatics clumpp population-genetics shell-script structure
Last synced: 2 months ago
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Pipelines to run STRUCTURE using multiple front-ends (CLUMPAK+StrAuto, Structure_threader)
- Host: GitHub
- URL: https://github.com/hernanmd/structurepipelines
- Owner: hernanmd
- Created: 2019-02-05T05:35:55.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-10-05T21:48:32.000Z (over 4 years ago)
- Last Synced: 2024-05-01T14:12:36.486Z (8 months ago)
- Topics: bioinformatics, clumpp, population-genetics, shell-script, structure
- Language: Shell
- Homepage:
- Size: 29.3 KB
- Stars: 8
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Table of Contents
- [Description](#description)
- [General Installation](#general-installation)
- [Pipeline CLUMPAK(StrAuto) + distruct](#pipeline-clumpakstrauto--distruct)
- [Requirements](#requirements)
- [Usage](#usage)
- [Download CLUMPAK](#download-clumpak)
- [Run Main Pipeline (CLUMPAK)](#run-main-pipeline-clumpak)
- [Run Distruct for many Ks](#run-distruct-for-many-ks)
- [Pipeline Structure_threader](#pipeline-structure_threader)
- [Installation](#installation)
- [Usage](#usage-1)
- [Create a "popfile"](#create-a-popfile)
- [Edit the "mainparams" and optionally the "extraparams" file](#edit-the-mainparams-and-optionally-the-extraparams-file)
- [Run analysis](#run-analysis)
- [Plot results](#plot-results)
- [Pipeline fastSTRUCTURE with Docker](#pipeline-faststructure-with-docker)
- [Installation](#installation-1)
- [Run image under Windows MSYS2 or WSL](#run-image-under-windows-msys2-or-wsl)
- [Run image under Linux/OSX](#run-image-under-linuxosx)
# Description
This repository contains three pipelines with scripts to run locally several types of STRUCTURE analysis :
- Pipeline [CLUMPAK](http://clumpak.tau.ac.il/index.html) analysis of STRUCTURE results produced by [StrAuto](https://www.crypticlineage.net/software/strauto/) and generate [distruct](https://www.crypticlineage.net/software/distruct/) figures.
- Pipeline Structure_threader with fastStructure
- Pipeline fastStructure with Docker
# General Installation
```bash
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:
```bash
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
```bash
./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
```bash
./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
```bash
./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"
```bash
# 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:
```bash
./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](https://hub.docker.com/r/dockerbiotools/faststructure)
```bash
docker pull dockerbiotools/faststructure
```
## Run image under Windows MSYS2 or WSL
```bash
# 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 /${PWD}/data/:/fastStructure/data 6ca
```
## Run image under Linux/OSX
```bash
# Get the image id from the following command
docker images
# Run the image
docker run -it -v /${PWD}/data/:/fastStructure/data 6ca
```