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INSTALL
View file @ ab456e42
# Installation
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), HomeBrew (OSX) or LinuxBrew.
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda.
* Linux - Ubuntu/Debian
* Linux - CentOS/RHEL
* Linux - using LinuxBrew
* OSX - using HomeBrew
* OSX/Linux - using Bioconda
* OSX/Linux - from source
* OSX/Linux - from a release tarball
......@@ -14,34 +12,18 @@ If you have a recent version of Ubuntu or Debian then you can install it using a
apt-get install snp-sites
```
## Linux - CentOS/RHEL
The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
## OSX/Linux - using Bioconda
Install Conda and install the bioconda channels.
```
sudo yum install epel-release gcc gcc-c++ automake ruby-irb
```
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
brew install snp-sites
```
## Linux - using LinuxBrew
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
brew install snp-sites
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install snp-sites
```
## OSX - using HomeBrew
Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
```
brew tap homebrew/science
brew install snp-sites
```
## OSX/Linux - from source
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).
```
autoreconf -i -f
......@@ -51,7 +33,7 @@ sudo make install
```
## OSX/Linux - from a release tarball
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
```
tar xzvf snp-sites-x.y.z.tar.gz
......@@ -60,3 +42,7 @@ cd snp-sites-x.y.z
make
sudo make install
```
## All platforms - Docker
Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites
README.md
View file @ ab456e42
[![Build Status](https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master)](https://travis-ci.org/sanger-pathogens/snp-sites)
# SNP-sites
Rapidly extracts SNPs from a multi-FASTA alignment.
[![Build Status](https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master)](https://travis-ci.org/sanger-pathogens/snp-sites)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE)
[![status](https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000056-brightgreen.svg)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056)
## Contents
* [Introduction](#introduction)
* [Installation](#installation)
* [Linux \- Ubuntu/Debian](#linux---ubuntudebian)
* [OSX/Linux \- using Bioconda](#osxlinux---using-bioconda)
* [OSX/Linux \- from source](#osxlinux---from-source)
* [OSX/Linux \- from a release tarball](#osxlinux---from-a-release-tarball)
* [All platforms \- Docker](#all-platforms---docker)
* [Usage](#usage)
* [Example input](#example-input)
* [Example usage](#example-usage)
* [Output](#output)
* [License](#license)
* [Feedback/Issues](#feedbackissues)
* [Citation](#citation)
## Introduction
Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
The software can be cited as:
## Installation
There are a few ways to install SNP-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda. If you encounter an issue when installing SNP-sites please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/snp-sites/issues) or email us at snpsites-help@sanger.ac.uk
* Linux - Ubuntu/Debian
* OSX/Linux - using Bioconda
* OSX/Linux - from source
* OSX/Linux - from a release tarball
### Linux - Ubuntu/Debian
If you have a recent version of Ubuntu or Debian then you can install it using apt.
```
apt-get install snp-sites
```
### OSX/Linux - using Bioconda
Install Conda and install the bioconda channels.
```
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install snp-sites
```
### OSX/Linux - from source
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa\
ke, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).
```
autoreconf -i -f
./configure
make
sudo make install
```
["SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)](http://dx.doi.org/10.1099/mgen.0.000056)
### OSX/Linux - from a release tarball
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa\
ke, autoconf, libtool).
```
tar xzvf snp-sites-x.y.z.tar.gz
cd snp-sites-x.y.z
./configure
make
sudo make install
```
### All platforms - Docker
Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites
## Usage
```
Usage: snp-sites [-mvph] [-o output_filename] <file>
......@@ -13,7 +83,9 @@ This program finds snp sites from a multi fasta alignment file.
-m output a multi fasta alignment file (default)
-v output a VCF file
-p output a phylip file
-o specify an output filename
-o STR specify an output filename [STDOUT]
-c only output columns containing exclusively ACGT
-b output monomorphic sites, used for BEAST
-h this help message
-V print version and exit
<file> input alignment file which can optionally be gzipped
......@@ -51,79 +123,20 @@ AGT
snp-sites my_alignment.aln
snp-sites my_gzipped_alignment.aln.gz
```
### Output
* Multi Fasta Alignment - Similar to the input file but just containing the SNP sites.
### Multi Fasta Alignment
Similar to the input file but just containing the SNP sites.
### VCF
This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.
### Relaxed Phylip format
All the SNP sites in a format for RAxML and other tree building applications.
# Installation
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), HomeBrew (OSX) or LinuxBrew.
* Linux - Ubuntu/Debian
* Linux - CentOS/RHEL
* Linux - using LinuxBrew
* OSX - using HomeBrew
* OSX/Linux - from source
* OSX/Linux - from a release tarball
* Windows/OSX/Linux - using a Virtual Machine
## Linux - Ubuntu/Debian
If you have a recent version of Ubuntu or Debian then you can install it using apt.
```
apt-get install snp-sites
```
## Linux - CentOS/RHEL
The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
```
sudo yum install epel-release gcc gcc-c++ automake ruby-irb
```
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
brew install snp-sites
```
## Linux - using LinuxBrew
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
brew install snp-sites
```
* VCF - This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.
## OSX - using HomeBrew
Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
```
brew tap homebrew/science
brew install snp-sites
```
## OSX/Linux - from source
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).
* Relaxed Phylip format - All the SNP sites in a format for RAxML and other tree building applications.
```
autoreconf -i -f
./configure
make
sudo make install
```
## License
SNP-sites is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE).
## OSX/Linux - from a release tarball
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
## Feedback/Issues
Please report any issues to the [issues page](https://github.com/sanger-pathogens/snp-sites/issues) or email snpsites-help@sanger.ac.uk
```
tar xzvf snp-sites-x.y.z.tar.gz
cd snp-sites-x.y.z
./configure
make
sudo make install
```
## Citation
If you use this software please cite:
## Windows/OSX/Linux - using a Virtual Machine
A virtual machine (VM) is available containing the software. More details can be found on [the Pathogen VM page](http://sanger-pathogens.github.io/pathogens-vm/).
"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, [Microbial Genomics 2(4), (2016)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056)
\ No newline at end of file
debian/changelog
View file @ ab456e42
snp-sites (2.4.0-1) UNRELEASED; urgency=medium
* New upstream version.
* Adjust watchfile to allow 'v' in version tags.
* Update upstream metadata (thanks Steffen Moeller).
-- Sascha Steinbiss <satta@debian.org> Thu, 14 Jun 2018 17:29:53 +0200
snp-sites (2.3.3-2) unstable; urgency=medium
* Upload to unstable.
......
debian/watch
View file @ ab456e42
version=4
https://github.com/sanger-pathogens/snp-sites/tags \
/sanger-pathogens/snp-sites/archive/([.\d]+)\.tar\.gz
/sanger-pathogens/snp-sites/archive/v?([.\d]+)\.tar\.gz
src/main.c
View file @ ab456e42
......@@ -38,7 +38,7 @@ static void print_usage()
printf(" -m output a multi fasta alignment file (default)\n");
printf(" -v output a VCF file\n");
printf(" -p output a phylip file\n");
printf(" -o STR specify an output filename\n");
printf(" -o STR specify an output filename [STDOUT]\n");
printf(" -c only output columns containing exclusively ACGT\n");
printf(" -b output monomorphic sites, used for BEAST\n");
printf(" -h this help message\n");
......@@ -62,7 +62,7 @@ static void print_version()
int main (int argc, char **argv) {
char multi_fasta_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {"/dev/stdout"};
int c;
int index;
......