Install Nonpareil

Nonpareil can be installed using conda, as a Biocontainer, with Galaxy, through Homebrew or via the source code.

Conda installation

Install Miniconda

Configure the channels to access Bioconda:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Install Nonpareil:
```
conda install nonpareil
```

Biocontainer

Install Docker

Pull the container:

$ docker pull quay.io/biocontainers/nonpareil

Launch the container:

$ docker run -i -t quay.io/biocontainers/nonpareil /bin/bash

Galaxy

You can install Nonpareil on your own Galaxy instance:

Go the Galaxy admin space
Search on the main Toolshed for the nonpareil repository available under the “Metagenomics” sections
Install it

It will automatically install Nonpareil via the conda installation

Homebrew

You can install Nonpareil using Homebrew <https://brew.sh> or Linuxbrew <http://linuxbrew.sh/>.

Install Homebrew <https://brew.sh> if you haven’t yet:

$ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Get the brewsci/bio <https://brewsci.github.io/homebrew-bio/> tap if you haven’t yet:
```
$ brew tap brewsci/bio
```
Install Nonpareil:
```
$ brew install nonpareil
```

Source code installation

System requirements

Nonpareil binary: Nonpareil requires a C++ compiler. It has been tested on 64-bit machines with GCC versions >=4.2.1, running Mac OSX and Red Hat Linux.

Nonpareil MPI: If you want to compile Nonpareil with MPI support, you will need OpenMPI (v > 1.4.3 tested). Other implementations of MPI could work, but are yet untested.

Nonpareil utilities: Requires R. No additional libraries are necessary.

Compilation

Get the source

Clone the repository from GitHub:
```
git clone git://github.com/lmrodriguezr/nonpareil.git
```
If you don’t have git, you can also download the TAR-Ball and unpack it with:
```
tar zxvf nonpareil.tar.gz
```
Compile

Change directory into the newly created folder, and compile Nonpareil:
```
cd nonpareil
make
```
If you want to compile Nonpareil MPI (see also MPI support), just run:
```
make nonpareil-mpi
```
In either case, you can specify the C++ compiler to be used setting the cpp or mpicpp variables, respectively. For example:
```
# This compiles nonpareil with /usr/local/bin/g++
make cpp=/usr/local/bin/g++ nonpareil
# This compiles nonpareil-mpi with /usr/local/bin/mpic++
make mpicpp=/usr/local/bin/mpic++ nonpareil-mpi
```
Install

If you want to make Nonpareil available system-wide, just run:
```
sudo make install
```
If you don’t have superuser privileges and/or want to install Nonpareil in a location other than /usr/local, simply set the prefix, for example:
```
make prefix=$HOME/apps install
```
You can also change the location of R, if it’s not in the $PATH or you want to use a non-standard installation:
```
make prefix=$HOME R=~/bin/R install
```
Other variables you can set explicitly for the install target are bindir (binaries directory) and mandir (documentation directory).