--- a/setup.py	Wed Sep 13 15:11:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-'''
-chimerascan
-
-Created on Jan 5, 2011
-
-@author: mkiyer
-'''
-from distutils.core import setup
-from distutils.extension import Extension
-
-import os
-import glob
-
-# local imports
-import chimerascan
-
-# ------ Setup instructions -------------------------------------------------
-
-setup_kwargs = {"name": "chimerascan",
-                "version": chimerascan.__version__,
-                "description": "chimeric transcript discovery from RNA-seq",
-                "long_description": __doc__,
-                "author": "Matthew Iyer",
-                "author_email": "mkiyer@umich.edu",
-                "license": "GPL3",
-                "platforms": "Linux",
-                "url": "http://chimerascan.googlecode.com",
-                "packages": ["chimerascan",
-                             "chimerascan.pysam",
-                             "chimerascan.bx",
-                             "chimerascan.pipeline",
-                             "chimerascan.lib",
-                             "chimerascan.tools"],
-                "package_data": {'chimerascan.tools': ['table_template.html']},                             
-                "scripts": ["chimerascan/chimerascan_run.py",
-                            "chimerascan/chimerascan_index.py",
-                            "chimerascan/tools/chimerascan_html_table.py",
-                            "chimerascan/tools/gtf_to_genepred.py",
-                            "chimerascan/tools/make_false_positive_file.py"]}
-
-# ---- Extension Modules ----------------------------------------------------
-
-def get_cython_extension_modules():
-    # pysam - samtools
-    samtools = Extension("chimerascan.pysam.csamtools", # name of extension
-                         ["chimerascan/pysam/csamtools.pyx",
-                          "chimerascan/pysam/pysam_util.c"] +\
-                          glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
-                          library_dirs=[],
-                          include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
-                          libraries=[ "z", ],
-                          language="c",
-                          define_macros = [('FILE_OFFSET_BITS','64'),
-                                           ('_USE_KNETFILE','')])     
-    # pysam - tabix
-    tabix = Extension("chimerascan.pysam.ctabix", # name of extension
-                      ["chimerascan/pysam/ctabix.pyx" ]  +\
-                      glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
-                      library_dirs=[],
-                      include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
-                      libraries=[ "z", ],
-                      language="c",
-                      )
-    # Interval clustering                
-    bx_cluster = Extension("chimerascan.bx.cluster", 
-                           ["chimerascan/bx/cluster.pyx", "chimerascan/bx/intervalcluster.c"], 
-                           include_dirs=["chimerascan/bx"])
-    # Interval intersection
-    bx_interval = Extension("chimerascan.bx.intersection",
-                            ["chimerascan/bx/intersection.pyx" ])
-    return [samtools, tabix, bx_cluster, bx_interval]
-
-def get_c_extension_modules():
-    # pysam - samtools
-    samtools = Extension("chimerascan.pysam.csamtools", # name of extension
-                         ["chimerascan/pysam/csamtools.c",
-                          "chimerascan/pysam/pysam_util.c"] +\
-                          glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
-                          library_dirs=[],
-                          include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
-                          libraries=[ "z", ],
-                          language="c",
-                          define_macros = [('FILE_OFFSET_BITS','64'),
-                                           ('_USE_KNETFILE','')])     
-    # pysam - tabix
-    tabix = Extension("chimerascan.pysam.ctabix", # name of extension
-                      ["chimerascan/pysam/ctabix.c" ]  +\
-                      glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
-                      library_dirs=[],
-                      include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
-                      libraries=[ "z", ],
-                      language="c",
-                      )
-    # Interval clustering                
-    bx_cluster = Extension("chimerascan.bx.cluster", 
-                           ["chimerascan/bx/cluster.c", "chimerascan/bx/intervalcluster.c"], 
-                           include_dirs=["chimerascan/bx"])
-    # Interval intersection
-    bx_interval = Extension("chimerascan.bx.intersection",
-                            ["chimerascan/bx/intersection.c"])
-    return [samtools, tabix, bx_cluster, bx_interval]
-
-def main():
-    setup(ext_modules=get_c_extension_modules(),
-          **setup_kwargs)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file