New upstream version 3.0.1

# Change log

All notable changes to this project will be documented in this file.

## Version 3.0.1 2019-08-01

#### TRANSIT:

 - Add check for python3 (TRANSIT 3+ requires python3.6+)

 - Minor fixes in GI and Pathway Enrichment

## Version 3.0.0 2019-07-18

#### TRANSIT:

 - TRANSIT now supports python 3. (To use with python 2, use releases < 3.0.0)

From r-base:3.4.1

RUN apt-get update -y && apt-get install -y -f python2 python-dev python-pip

From r-base:3.6.1

RUN apt-get update -y && apt-get install -y -f python3 python-dev python3-pip

ADD src/ /src

ADD tests/ /tests

RUN pip install pytest 'numpy~=1.15' 'scipy~=1.2' 'matplotlib~=2.2' 'pillow~=5.0' 'statsmodels~=0.9' 'rpy2<2.9.0'

RUN pip3 install pytest 'numpy~=1.16' 'scipy~=1.2' 'matplotlib~=3.0' 'pillow~=6.0' 'statsmodels~=0.9' 'rpy2'

RUN R -e "install.packages('MASS')"

RUN R -e "install.packages('pscl')"

# TRANSIT

[![Version](https://img.shields.io/github/tag/mad-lab/transit.svg)](https://github.com/mad-lab/transit)   [![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest)   [![Downloads](https://pepy.tech/badge/tnseq-transit)](https://pepy.tech/project/tnseq-transit)

=======

**NOTE: TRANSIT v3.0+ now requires python3.6+. If you want to use TRANSIT with python2, use version < 3.0.**

Welcome! This is the distribution for the TRANSIT and TPP tools developed by the [Ioerger Lab](http://orca2.tamu.edu/tom/iLab.html) at Texas A&M University.

TRANSIT is a tool for processing and statistical analysis of Tn-Seq data.

-   Ability to analyze datasets from libraries constructed using  **himar1 or tn5 transposons**.

-   **TrackView** to help visualize read-counts accross the genome.

-   **TrackView** to help visualize read-counts across the genome.

-   Can **export datasets** into a variety of formats, including **IGV**.

    description='TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.',

    long_description=long_description,

    long_description_content_type='text/markdown',

    # The project's main homepage.

    url='https://github.com/mad-lab/transit',

    main(*args, **kwargs)

def main(*args, **kwargs):

    # Check python version

    if (sys.version_info[0] < 3):

        print("TRANSIT v3.0+ requires python3.6+. To use with python2, please install TRANSIT version < 3.0")

        sys.exit(0)

    vars = Globals()

    # Check for arguements

    if not args and not kwargs and hasWx: