Install Nonpareil¶

Nonpareil can be installed using conda, as a Biocontainer, with Galaxy, through Homebrew <https://brew.sh> 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:

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

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:
```
make cpp=/usr/local/bin/g++ nonpareil # This compiles nonpareil with /usr/local/bin/g++
make mpicpp=/usr/local/bin/mpic++ nonpareil-mpi # This compiles nonpareil-mpi with /usr/local/bin/mpic++
```
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).