diff --git a/.travis.yml b/.travis.yml index 3686a68..d2d1168 100644 --- a/.travis.yml +++ b/.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=$TRAVIS_PYTHON_VERSION numpy matplotlib click reportlab pandas pyyaml - - source activate DeNovoPipeline - python setup.py develop script: diff --git a/README.md b/README.md index 513a62e..dd89b95 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ The pipeline is structured in three different sub-pipelines, and a number of con ## Installation -NouGAT is a python package. From a practical point of view it is a wrapper around a certain number of tools that allow to perform de novo assembly analysis. In order to install NouGAT the following steps must be followed: +NouGAT is a python package. From a practical point of view it is a wrapper around a certain number of tools that allow to perform de novo assembly analysis. We recommend creating a Conda virtual environment for installing NouGAT: ```bash # First we create a new virtual python environment using conda, get it here: diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..a617cc3 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,7 @@ +reportlab>=3.1.8 +pandas>=0.14.0 +numpy>=1.8.1 +matplotlib>=1.4.3 +reportlab>=3.1.8 +pyyaml>=3.11 +click>=5.0 diff --git a/sciLifeLab_utils/README.md b/sciLifeLab_utils/README.md index 22c7817..4c30845 100644 --- a/sciLifeLab_utils/README.md +++ b/sciLifeLab_utils/README.md @@ -4,14 +4,7 @@ ### Requirements * Fastq sequence data in the folder structure as delivered by [NGI Stockholm](https://portal.scilifelab.se/genomics/) * Needs to be run on [UPPMAX](http://www.uppmax.uu.se/). -* Python packages `reportlab` and `click` -### Installation -```bash -# Assuming NouGAT has been installed -source activate DeNovoPipeline -pip install reportlab click -``` The commandline tool `scilifelab_denovo` supports customizable parameter defaults for all it's sub-commands. It attempts to read a [configuration file](../config_files/scilifelab.conf) found in the file `$HOME/.nougat/scilifelab.conf`. ```bash diff --git a/setup.py b/setup.py index 315cafb..115ca25 100644 --- a/setup.py +++ b/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='francesco.vezzi@scilifelab.se', 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 )