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treangen committed Feb 10, 2015
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![Travis-CI build status]
(https://travis-ci.org/marbl/parsnp.svg?branch=master)
Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite :

# Parsnp
- [Harvest project page](http://harvest.readthedocs.org)
- url: http://harvest.readthedocs.org

Rapid bacterial core genome alignment and SNP detection
Parsnp is primarily distributed as a binary for Linux or OS X (see Parsnp link above ). However, the source and build scripts are provided for incompatible platforms or for development purposes.

## Download, install & run (precompiled binary)
CITATION provides details on how to cite Parsnp.

Parsnp is distributed as a precompiled binary that should be devoid of external dependencies (all included in dist). The steps below represent the fastest way to start using the software:
INSTALL provides instructions for building from source and installing.

### On OSX:

1. wget https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-OSX64-v1.0.tar.gz
2. unzip -d parsnp-OSX64.gz

### On Linux:


1. wget https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-Linux64-v1.0.tar.gz
2. unzip -d parsnp-Linux64.gz


### Quick start

parsnp –p <threads> –d <directory of genomes> –r <ref genome>

Output Files:

1) Newick formatted core genome SNP tree: <outdir>/parsnp.tree
2) XMFA format: <outdir>/parsnp.xmfa
3) Gingr input: <outdir>/parsnp.ggr
4) VCF variants: <outdir>/parsnp.vcf


## Build from source

### Important! Prerequisites required for building from source, install these first:

* 64-bit Linux/*nix or OSX (>= v10.7)
* autoconf && automake && libtool
* gcc (>= v4.2.*)
* OpenMP
* Python (>= 2.6.*)
To install from source:
git clone https://github.com/marbl/parsnp.git parsnp_src
cd parsnp_src
Before you start, if running OSX Mavericks, OpenMP is not supported via Clang, so you will not be able to build the source. You will need to install OpenMP and build gcc with OpenMP support. This can be accomplished a couple of ways:
* Install Macports, then:
- sudo port install gcc49
- sudo port select gcc mp-gcc49
* (or) Install Homebrew, then:
- brew install gcc49
* (or) Build & install gcc from source with OpenMP
- Download & install gcc 4.9
- https://gcc.gnu.org/install/
* (or) Download & install gcc prebuilt binaries with OpenMP support
- http://hpc.sourceforge.net/
* Final suggestion: If issues persist, we recommend using the precompiled binary until OpenMP is natively supported by Clang/OSX (likely to be so in Yosemite)
Once OpenMP support is added, the first (required!) step is to build libMUSCLE:
cd muscle
./autogen.sh
./configure --prefix=`pwd` CXXFLAGS=’-fopenmp’
make install
Then, build Parsnp:
cd ..
./autogen.sh
./configure
make install
Once both installed (to cwd install by default):
export PARSNPDIR=/path/to/parsnp/install
## External software dependencies:
* Muscle 3.8 (included as lib)
* PhiPack (Linux and OSX 64-bit binaries included in distribution)
* FastTree2 (Linux and OSX 64-bit binaries included in distribution)
## Docs
See http://harvest.readthedocs.org for full documentation
LICENSE provides licensing information.

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