Installation

IntegronFinder dependencies

IntegronFinder is built with Python 2.7, and a few libraries are needed:

  • Python 2.7
    • Pandas (>=0.18.0)
    • Numpy (>=1.9.1)
    • Biopython (>=1.65)
    • Matplotlib (>=1.4.3)

If you’re not at ease with Python, see here on how to install Python and its libraries

In addition, IntegronFinder has external dependencies which have to be installed prior the use of the program (click to access the corresponding website).

After installation of these programs, they should be in your $PATH (i.e. you can type in a terminal hmmsearch, cmsearch, or prodigal and a command not found shall not be displayed). If you have them installed somewhere else, please refers to the parameters to give complete path to IntegronFinder.

Installation procedure

  1. Download the latest release

  2. In a shell (e.g. a terminal), start installation with:

    (sudo) python pip install integron_finder-x.x.tar.gz

Note

Super-user privileges (i.e., sudo) are necesserary if you want to install the program in the general file architecture.

Note

If you do not have the privileges, or if you do not want to install IntegronFinder in the Python libraries of your system, you can install IntegronFinder in a virtual environment. See virtualenv or if you’re using Canopy, see Canopy CLI

Warning

When installing a new version of IntegronFinder, do not forget to uninstall the previous version installed !

Warning

The installer does not work with pure setuptools procedure, it does not work in egg. Unless you disable egg by using the --root option. python setup.py install --root /prefix/where/to/install/integron_finder

Uninstallation procedure

To uninstall integron_finder, run in the following command:

(sudo) pip uninstall integron_finder

It will uninstall integron_finder executable

How to install Python

The purpose of this section is to provide some help about installing python dependencies for IntegronFinder if you never installed any python package.

As IntegronFinder has not been test on Windows, we assume Unix-based operating system. For Windows users, the best would be to install a unix virtual machine on your computer.

Usually a python distribution is already installed on your machine. However, if you don’t know how to install libraries, we recommend to re-install it from a distribution which contains pre-compiled libraries. There are two main distributions (click to access website):

Download version 2.7 which correspond to your machine, then make sure that python from these distributions is the default one (you can possibly choose that in the preference and/or during installation). They both come with all the needed packages but Biopython. If you have a student email adress from a university-delivering degree, you can request an academic licence to Enthough Canopy (see Canopy for Academics) which will allow you to download additional packages including Biopython.

Otherwise, you will have to install Biopython manually. pip is recommended as a python packages installer. It works as follow:

(sudo) pip install Biopython==1.65

To install version 1.65 of Biopython (recommended for IntegronFinder).

Note

If you don’t manage to install all the packages, try googling the error, or don’t hesisate to ask a question on stackoverflow.