old_contents: #!/usr/bin/env python
  """Setup file and install script for NextGen sequencing analysis scripts.
  """
  import os
  from setuptools import setup, find_packages
  
  version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline', 'version.py')
  version = open(version_py).read().strip().split('=')[-1].replace('"','')
  
  setup(name = "bcbio-nextgen",
        version = version,
        author = "Brad Chapman",
        author_email = "chapmanb@50mail.com",
        description = "Best-practice pipelines for fully automated high throughput sequencing analysis",
        license = "MIT",
        url = "https://github.com/chapmanb/bcbio-nextgen",
        namespace_packages = ["bcbio"],
        dependency_links = ['http://github.com/ipython/ipython/tarball/master#egg=ipython-1.0.dev'],
        packages = find_packages(),
        package_data={'bcbio': ['bam/data/*']},
        scripts = ['scripts/bcbio_nextgen.py',
                   'scripts/bam_to_wiggle.py',
                   'scripts/barcode_sort_trim.py',
                   'scripts/illumina_finished_msg.py',
                   'scripts/nextgen_analysis_server.py',
                   'scripts/solexa_qseq_to_fastq.py',
                   ],
        install_requires = [
            "bioblend >= 0.2.4",
            "biopython >= 1.61",
            "boto >= 2.8.0",
            "cutadapt >= 1.2.1",
            "Cython >= 0.18",
            "fabric >= 1.6.0",
            "ipython >= 1.0.dev",
            "ipython-cluster-helper >= 0.1.7",
            "Logbook >= 0.4.1",
            "Mako >= 0.7.3",
            "pybedtools >= 0.6.2",
            "py_descriptive_statistics >= 0.2",
            "psutil >= 0.6.1",
            "pysam >= 0.7.4",
            "PyYAML >= 3.10",
            "pyzmq >= 13.1.0",
            "futures >= 2.1.4",
            "sh >= 1.07",
            #"paramiko >= 1.9.0",
            #"celery >= 2.2.7,<3.0.0",
            #"rpy2 >= 2.0.7"
        ])
  
new_contents: #!/usr/bin/env python
  """Setup file and install script for NextGen sequencing analysis scripts.
  """
  import os
  from setuptools import setup, find_packages
  
  version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline', 'version.py')
  version = open(version_py).read().strip().split('=')[-1].replace('"','')
  
  setup(name = "bcbio-nextgen",
        version = version,
        author = "Brad Chapman",
        author_email = "chapmanb@50mail.com",
        description = "Best-practice pipelines for fully automated high throughput sequencing analysis",
        license = "MIT",
        url = "https://github.com/chapmanb/bcbio-nextgen",
        namespace_packages = ["bcbio"],
        dependency_links = ['http://github.com/ipython/ipython/tarball/master#egg=ipython-1.0.dev'],
        packages = find_packages(),
        package_data={'bcbio': ['bam/data/*']},
        zip_safe=False,
        scripts = ['scripts/bcbio_nextgen.py',
                   'scripts/bam_to_wiggle.py',
                   'scripts/barcode_sort_trim.py',
                   'scripts/illumina_finished_msg.py',
                   'scripts/nextgen_analysis_server.py',
                   'scripts/solexa_qseq_to_fastq.py',
                   ],
        install_requires = [
            "bioblend >= 0.2.4",
            "biopython >= 1.61",
            "boto >= 2.8.0",
            "cutadapt >= 1.2.1",
            "Cython >= 0.18",
            "fabric >= 1.6.0",
            "ipython >= 1.0.dev",
            "ipython-cluster-helper >= 0.1.7",
            "Logbook >= 0.4.1",
            "Mako >= 0.7.3",
            "pybedtools >= 0.6.2",
            "py_descriptive_statistics >= 0.2",
            "psutil >= 0.6.1",
            "pysam >= 0.7.4",
            "PyYAML >= 3.10",
            "pyzmq >= 13.1.0",
            "futures >= 2.1.4",
            "sh >= 1.07",
            #"paramiko >= 1.9.0",
            #"celery >= 2.2.7,<3.0.0",
            #"rpy2 >= 2.0.7"
        ])
  
subject: Use zip_safe=False to keep the installation unzipped for easier debugging. Fixes issue #41.