--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/setup.py	Tue Sep 12 13:57:02 2017 -0400
@@ -0,0 +1,108 @@
+'''
+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()
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