[med-svn] [Git][med-team/snp-sites][master] 5 commits: fix watchfile
Sascha Steinbiss
gitlab at salsa.debian.org
Thu Jun 14 16:36:26 BST 2018
Sascha Steinbiss pushed to branch master at Debian Med / snp-sites
Commits:
45265ace by Sascha Steinbiss at 2018-06-14T17:30:51+02:00
fix watchfile
- - - - -
fa7d887c by Sascha Steinbiss at 2018-06-14T17:31:09+02:00
New upstream version 2.4.0
- - - - -
fafcb545 by Sascha Steinbiss at 2018-06-14T17:31:14+02:00
Update upstream source from tag 'upstream/2.4.0'
Update to upstream version '2.4.0'
with Debian dir add7382a3187fdb173198b31f5c39acd53cd24db
- - - - -
412d6141 by Sascha Steinbiss at 2018-06-14T17:33:21+02:00
new upstream version
- - - - -
ab456e42 by Sascha Steinbiss at 2018-06-14T17:36:02+02:00
mark as UNRELEASED
- - - - -
6 changed files:
- INSTALL
- README.md
- VERSION
- debian/changelog
- debian/watch
- src/main.c
Changes:
=====================================
INSTALL
=====================================
--- a/INSTALL
+++ b/INSTALL
@@ -1,10 +1,8 @@
# 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
@@ -59,4 +41,8 @@ cd snp-sites-x.y.z
./configure
make
sudo make install
-```
\ No newline at end of file
+```
+
+## 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
=====================================
--- a/README.md
+++ b/README.md
@@ -1,22 +1,94 @@
-[](https://travis-ci.org/sanger-pathogens/snp-sites)
# SNP-sites
+Rapidly extracts SNPs from a multi-FASTA alignment.
+
+[](https://travis-ci.org/sanger-pathogens/snp-sites)
+[](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE)
+[](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 at 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>
This program finds snp sites from a multi fasta alignment file.
- -r output internal pseudo reference sequence
- -m output a multi fasta alignment file (default)
- -v output a VCF file
- -p output a phylip file
- -o specify an output filename
- -h this help message
- -V print version and exit
- <file> input alignment file which can optionally be gzipped
+ -r output internal pseudo reference sequence
+ -m output a multi fasta alignment file (default)
+ -v output a VCF file
+ -p output a phylip file
+ -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
```
This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:
@@ -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 at 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
=====================================
VERSION
=====================================
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.3
+2.4.0
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+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 at debian.org> Thu, 14 Jun 2018 17:29:53 +0200
+
snp-sites (2.3.3-2) unstable; urgency=medium
* Upload to unstable.
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,3 @@
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
=====================================
--- a/src/main.c
+++ b/src/main.c
@@ -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;
View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef
--
View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef
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