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setup.py
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setup.py
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import setuptools
from setuptools.command.install import install
# Install Necessary R packages
class CustomInstallPackages(install):
"""Customized setuptools install command - runs R package install one-liner."""
def run(self):
import subprocess
import shlex
print "Attempting to install R packages...Please wait."
cmd =''' R -e "install.packages(c('optparse', 'gtools', 'klaR','survival', 'mvtnorm', 'modeltools', 'coin', 'MASS'), repos = 'http://cran.stat.ucla.edu')" '''
try:
subprocess.call(shlex.split(cmd))
print "Necessary R packages were sucessfully installed"
except:
print "Error installing R dependecies! Check to see if R is properly installed or see online documentation for more answers."
install.run(self)
# Pkg info
setuptools.setup(
name="koeken",
version="0.2.6",
url="https://github.com/twbattaglia/koeken",
author="Thomas W. Battaglia",
author_email="tb1280@nyu.edu",
description="A Linear Discriminant Analysis (LEfSe) wrapper.",
long_description=open('README.rst').read(),
keywords="Biology Microbiome LEfSe QIIME Formatting Diversity Python Bioinformatics",
scripts=['koeken/koeken.py', 'koeken/lefse_src/format_input.py', 'koeken/lefse_src/run_lefse.py', 'koeken/lefse_src/lefse.py', 'koeken/lefse_src/plot_cladogram.py', 'koeken/lefse_src/hclust2/hclust2.py', 'koeken/pretty_lefse.py'],
cmdclass={'install': CustomInstallPackages},
packages=setuptools.find_packages(),
install_requires=['rpy2', 'argparse', 'pandas', 'biopython'],
classifiers=[
'Development Status :: 2 - Pre-Alpha',
'Programming Language :: Python',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.4'
]
)