Install Nonpareil

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

Conda installation

  1. Install Miniconda

  2. Configure the channels to access Bioconda:

    $ conda config --add channels defaults
    $ conda config --add channels conda-forge
    $ conda config --add channels bioconda
    
  3. Install Nonpareil:

    $ conda install nonpareil
    

Biocontainer

  1. Install Docker

  2. Pull the container:

    $ docker pull quay.io/biocontainers/nonpareil
    
  3. Launch the container:

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

Galaxy

You can install Nonpareil on your own Galaxy instance:

  1. Go the Galaxy admin space
  2. Search on the main Toolshed for the nonpareil repository available under the “Metagenomics” sections
  3. Install it
It will automatically install Nonpareil via the conda installation

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

  1. 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
    
  2. 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++
    
  3. 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).