Make dependencies more explicit

.travis.yml

@@ -5,17 +5,7 @@ python:
 notifications:
   email: false
 
-# Setup anaconda
-before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=$HOME/miniconda2/bin:$PATH
-  - conda update -y -q conda
-# Install packages
 install:
-  - conda create -q -y -n DeNovoPipeline python=$TRAVIS_PYTHON_VERSION numpy matplotlib click reportlab pandas pyyaml
-  - source activate DeNovoPipeline
   - python setup.py develop
 
 script:

README.md

@@ -22,7 +22,7 @@ The pipeline is structured in three different sub-pipelines, and a number of con
 
 
 ## Installation
-NouGAT is a python package. From a practical point of view it is a wrapper around a certain number of tools that allow to perform de novo assembly analysis. In order to install NouGAT the following steps must be followed:
+NouGAT is a python package. From a practical point of view it is a wrapper around a certain number of tools that allow to perform de novo assembly analysis. We recommend creating a Conda virtual environment for installing NouGAT:
 
 ```bash
 # First we create a new virtual python environment using conda, get it here: 

requirements.txt

@@ -0,0 +1,7 @@
+reportlab>=3.1.8
+pandas>=0.14.0
+numpy>=1.8.1
+matplotlib>=1.4.3
+reportlab>=3.1.8
+pyyaml>=3.11
+click>=5.0

sciLifeLab_utils/README.md

@@ -4,14 +4,7 @@
 ### Requirements
 * Fastq sequence data in the folder structure as delivered by [NGI Stockholm](https://portal.scilifelab.se/genomics/)
 * Needs to be run on [UPPMAX](http://www.uppmax.uu.se/). 
-* Python packages `reportlab` and `click`
 
-### Installation
-```bash
-# Assuming NouGAT has been installed
-source activate DeNovoPipeline
-pip install reportlab click
-```
 
 The commandline tool `scilifelab_denovo` supports customizable parameter defaults for all it's sub-commands. It attempts to read a [configuration file](../config_files/scilifelab.conf) found in the file `$HOME/.nougat/scilifelab.conf`.
 ```bash

setup.py

@@ -1,20 +1,28 @@
 #!/usr/bin/env python
-
 from setuptools import setup
 
+try:
+    with open("requirements.txt", "r") as f:
+        install_requires = [x.strip() for x in f.readlines()]
+except IOError:
+    install_requires = []
+
+
 setup(name='nougat',
-    version='0.5',
+    version='0.6',
     description= 'An automated analysis pipeline for de novo assembly',
     author='Francesco Vezzi',
     author_email='[email protected]',
     url='https://github.com/SciLifeLab/NouGAT',
+    license='MIT',
     scripts=['nougat/deNovo_pipeline.py'],
     packages=['nougat'],
-    namespace_packages=["nougat"],
+    namespace_packages=['nougat'],
 
     entry_points={
         'console_scripts': [
             'scilifelab_denovo = sciLifeLab_utils.run_denovo:main',
         ],
     },
+    install_requires=install_requires
 )