SeqFindR

HomePage: http://github.com/mscook/SeqFindR

Author: Mitchell Stanton-Cook

Download: https://pypi.python.org/packages/source/S/SeqFindR/SeqFindR-0.31.tar.gz

        SeqFindR
========

.. image:: https://travis-ci.org/mscook/SeqFindR.png?branch=master
        :target: https://travis-ci.org/mscook/SeqFindR

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.. image:: https://landscape.io/github/mscook/SeqFindR/master/landscape.png
   :target: https://landscape.io/github/mscook/SeqFindR/master
   :alt: Code Health


SeqFindR - easily create informative genomic feature plots.

Work in progress:
    * `SeqFindR documentation`_
    * `SeqFindR official site`_

**SeqFindR is nearing a stable API.** 

**We have only tested SeqFindR on linux systems.** There has been some 
success with `MacOSX`_. 

Best use "git log" for a changelog as the `changelog`_ for most recent 
changes/fixes/enhancements may not be up to date.


Cite this Github repository if you use SeqFindR to generate figures 
for publications:: 

    STANTON-COOK M, NF ALIKHAN, FORDE BM, BEN ZAKOUR NL & BEATSON SA^. 
    SeqFindR - easily create informative genomic feature plots.
    https://github.com/mscook/SeqFindR.


Quick install (Ubuntu)
----------------------

Simple install for Ubuntu/Debian systems::

    $ sudo apt-get install python-numpy python-scipy python-matplotlib python-biopython ncbi-blast+ python-dev python-pip libatlas-dev liblapack-dev gfortran libfreetype6-dev libfreetype6 libpng-dev git && cd ~/ && git clone https://github.com/mscook/SeqFindR.git && pip install -e SeqFindR/


Requirements
------------

You'll need to install/have installed:
    * ncbiblast >= 2.2.27
    * python >= 2.7 (**Python 3 is not supported**)
    * `pip`_
    * `git`_ (depending on your install route) 

You can check these are installed by::
    
    $ python --version
    $ which blastn
    $ which pip
    $ which git


The following python libraries should be installed automatically if you follow 
the installation instructions detailed below.

We use the following python `libraries`_:
    * numpy >= 1.6.1
    * scipy >= 0.10.1
    * matplotlib >= 1.1.0
    * biopython >= 1.59
    * ghalton>=0.6

These libraries will also have dependencies (i.e. atlas, lapack, fortran 
compilers, freetype and png).

The state of Python packaging (distribution of code) is that bad, you could 
miss many nights sleep. I'm looking at you SciPy. **For the smoothest possible 
install we recommend installing the requirements using your distributions 
package manager.** That is via apt-get, yum or similar.

For Ubuntu (fresh server install) you can get requirements using::

    $ sudo apt-get install python-numpy python-scipy python-matplotlib
    python-biopython ncbi-blast+ python-dev python-pip libatlas-dev
    liblapack-dev gfortran libfreetype6-dev libfreetype6 libpng-dev git


Installation (possibly painful)
-------------------------------

If you are a member of the Beatson Group you'll already have SeqFindR in your 
$PATH on barrine. You do not need to install SeqFindR. UQ based researchers 
should email me (m.stantoncook@gmail.com) for the location of SeqFindR.

Option 1a (with root/admin)::
    
    $ pip install SeqFindR

Option 1b (as a standard user)::

    $ pip install SeqFindR --user

This assumes you have pip installed (see `pip`_). The SciPy, NumPy and 
matplotlib installations will break if you are missing libraries such as 
atlas, lapack, fortran compilers, freetype and png).


**You'll need to have git installed** for the following alternative install 
options. git can be really useful for scientists. See `here`_ for some 
discussion. Installing this way will provide you with the most recent version 
of SeqFindR.

Option 2a (with root/admin & git)::

    $ cd ~/
    $ git clone git://github.com/mscook/SeqFindR.git
    $ cd SeqFindR
    $ sudo python setup.py install

Option 2b (standard user & git) **replacing INSTALL/HERE with appropriate**::

    $ cd ~/
    $ git clone git://github.com/mscook/SeqFindR.git
    $ cd SeqFindR
    $ echo 'export PYTHONPATH=$PYTHONPATH:~/INSTALL/HERE/lib/python2.7/site-packages' >> ~/.bashrc
    $ echo 'export PATH=$PATH:~/INSTALL/HERE/bin' >> ~/.bashrc
    $ source ~/.bashrc
    $ python setup.py install --prefix=~/INSTALL/HERE/SeqFindR/  
    

If