Installation

Easy install with pip

Local install (no sudo rights, recommended)

To install the module and the command line tools, without sudo rights, type (thanks to this post from Kaz’hack for installing without sudo rights):

pip install --user --upgrade git+https://github.com/matthieu-bruneaux/pygenbank

This will install the executables in ~/.local/bin/ and the Python module in ~/.local/lib/python2.7/site-packages/.

To run the executables from the command line, you might need to add ~/.local/bin/ to the $PATH variable in your ~/.bashrc file:

# Lines to add in your ~/.bashrc file, if needed
PATH=$PATH:~/.local/bin
export PATH

System-wide install (with sudo rights, use with care!)

If you want to install the module and the command line tools system-wide (i.e. accessible for anyone), you can run pip with sudo rights (this is not the recommended way to install!):

sudo pip install --upgrade git+https://github.com/matthieu-bruneaux/pygenbank

Test installation

You can test if the installation worked with:

pygenbank-search -h
pygenbank-extract-CDS -h

and from Python:

import genbank as gb
dir(gb)

Uninstall

To remove the module and the command line tools, type:

pip uninstall pygenbank -y

if pygenbank was installed without sudo rights. If it was installed with sudo rights, then you will need to use:

sudo pip uninstall pygenbank-y

Installation from a cloned repository

First, clone the GitHub repository:

git clone https://github.com/matthieu-bruneaux/pygenbank
cd pygenbank

A Makefile is provided with the Python project folder. Just type make to have a short summary of the different targets available.

To install the module:

make install

This will install the module for the current user (using pip install --user -e .). See above how to add ~/.local/bin to the PATH variable if the command line tools are not accessible after this install.

To remove the module:

make uninstall

You can also run some tests and regenerate the documentation:

make tests
make doc