python v2.7.* gcc gsl
These items are prerequisities for the installation of concoct as described below. The installation procedure varies on different systems, and described in this README is only how to proceed with a linux (ubuntu) distribution.
The first item, python v2.7.*, should be installed on a modern Ubuntu distribution. A c-compiler, e.g. gcc, is needed to compile the c parts of concoct that uses the GNU Scientific Library gsl. For linux (ubuntu) this is installed through:
apt-get install build-essential libgsl0-dev
cython>=0.19.2 numpy>=1.7.1 scipy>=0.12.0 pandas>=0.11.0 biopython>=1.62b scikit-learn>=0.13.1
These are the python packages that need to be installed in order to run concoct. If you follow the installation instructions below, these will be installed automatically, but are listed here for transparency.
- For assembly, use your favorite, here is one
- In velvet installation directory Makefile, set ‘MAXKMERLENGTH=128’, if this value is smaller in the default installation.
- To create the input table (containing average coverage per sample and contig)
- For validation of clustering using single-copy core genes
- Prodigal >= 2.60
- Python packages: bcbio-gff>=0.4
- R packages: gplots, reshape, ggplot2, ellipse, getopt and grid
If you want to install these dependencies on your own server, you can take a look at doc/Dockerfile.all_dep for ideas on how to install them.
Here we describe two recommended ways of getting concoct to run on your computer/server. The first option, using Anaconda, should work for any *nix (e.g. Mac OS X or Linux) system even where you do not have ‘sudo’ rights (e.g. on a common computer cluster). The second option is suitable for a linux computer where you have root privileges and you prefer to use a virtual machine where all dependencies to run concoct are included. Docker does also run on Mac OS X through a virtual machine. For more information check out the [Docker documentation](http://docs.docker.com/installation/).
This instruction shows how to install all dependencies (except the ‘Fundamental dependencies’ and the ‘Optional dependencies’ listed above) using an Anaconda environment. Anaconda is a tool to isolate your python installation, which allows you to have multiple parallel installations using different versions of different packages, and gives you a very convenient and fast way to install the most common scientific python packages. Anaconda is free but not open source, you can download Anaconda here. Installation instructions can be found here.
After installing Anaconda, create a new environment that will contain the concoct installation:
conda create -n concoct_env python=2.7.6
After choosing to proceed, run the suggested command:
source activate concoct_env
then install the concoct dependencies into this environment:
conda install cython numpy scipy biopython pandas pip scikit-learn
Finally, download the CONCOCT distribution from https://github.com/BinPro/CONCOCT/releases (stable) and extract the files, or clone the repository with github (potentially unstable). Resolve all dependencies, see above and then execute within the CONCOCT directory:
python setup.py install
If you have root access to a machine where you want to install concoct and you have storage for roughly 2G “virtual machine” then Docker provides a very nice way to get a Docker image with concoct and its dependencies installed. This way the only thing you install on your host system is Docker, the rest is contained in an Docker image. This allows you to install and run programs in that image without it affecting your host system. You should get to know Docker here. You need to get Docker installed and specially if you have Ubuntu. When Docker is installed you need to download and log into the concoct image.
We provide a Docker image:
binpro/concoct_latest contains CONCOCT and all its dependencies for the complete workflow with the exception of the SCG evaluation.
The following command will then download the image from the Docker image index, map the Data folder to the image and log you into the docker image.
sudo docker run -v /home/USER/Data:/opt/Data -i -t binpro/concoct_latest bash
To test concoct you can then do:
$ cd /opt/CONCOCT_latest $ nosetests
Which should execute all tests without errors.