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INSTALL.md

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Installation instructions for MetLab

MetLab requires a number of python modules to work properly, namely:

  • biopython
  • numpy
  • mpmath (optional)

To use the "metapprox" Experimental Design module for approximating sequencing need for metagenomic project - OSX users must either compile the c-extensions using the "install_dependencies.sh"-script, or by installing the mpmath python module.

MetLab installation was tested on Mac OSX 10.10.5, Ubuntu 14.04 and Centos 7.

Installing on OS X

To install the required python modules run the following commands in the terminal:

easy_install pip
pip install biopython
pip install numpy
pip install mpmath

Then run the included "install_dependencies.sh"-script to install dependencies that are not already in your PATH.

./install_dependencies.sh

Installing on Ubuntu

sudo apt-get install sqlite3 python-biopython python-tk
curl -O https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
sudo pip install numpy
sudo pip install mpmath

To build the metapprox module, you'll also need gmp, mpfr and python-dev:

sudo apt-get install libgmp3-dev libmpfr-dev python-dev

Then run the included "install_dependencies.sh"-script to install dependencies that are not already in your PATH.

./install_dependencies.sh

Installing on CentOS

sudo yum install ncurses-devel python-biopython tkinter
curl -O https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
sudo pip install mpmath

To build the metapprox module, you'll also need gmp, mpfr and python-dev:

sudo yum install gmp-devel mpfr-devel

Then run the included "install_dependencies.sh"-script to install dependencies that are not already in your PATH.

./install_dependencies.sh

Custom Kraken Databases

Although the default kraken database gives decent results, it was not designed with viruses in mind. We provide two databases enriched in Viruses.

Theses databases are built using combination of RefSeq (Archea + Bacteria) and the phages and viral divisions of GenBank. They can be found below:

Database size (tar.gz) size (unpacked)
superdb 42G 86.3G
mini superdb 4G 13.2G

Once downloaded, unpack the archive and modify the kraken_db path in the 'Run pipelines' module to point to the correct folder.