Adding setup.py for OptiType

.gitignore

@@ -1,4 +1,8 @@
 # Created by .gitignore support plugin (hsz.mobi)
 
 *.pyc
-.gitignore
+.gitignore
+
+# build/
+build/
+.venv/

bin/optitype

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+"""Entry point script for optitype package."""
+
+import optitype.OptiTypePipeline
+import sys
+
+if __name__ == '__main__':
+    sys.exit(optitype.OptiTypePipeline.main())

optitype/config.ini

@@ -0,0 +1,16 @@
+[MAPPING]
+# The following expects the "razers3" binary to be on your PATH, update
+# to provide a different path.
+RAZERS3=razers3
+THREADS=16
+
+[LIBRARIES]
+# Relative directories are relative to the module.
+RNA_REF=./data/hla_reference_rna.fasta
+DNA_REF=./data/hla_reference_dna.fasta
+ALLELES=./data/alleles.h5
+
+[OPTIMIZATION]
+# Using COIN-OR CBC by default, the solver has to be supported by Coopr
+SOLVER=cbc
+THREADS=1

model.py → optitype/model.py

@@ -12,7 +12,6 @@
 """
 
 from __future__ import division
-import coopr.environ
 from coopr.pyomo import ConcreteModel, Set, Param, Var, Binary, Objective, Constraint, ConstraintList, maximize
 from coopr.opt import SolverFactory
 from collections import defaultdict

setup.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+from distutils.core import setup
+
+setup(name='OptiType',
+      version='1.0',
+      description='Precision HLA typing from next-generation sequencing data',
+      author='Andras Szolek, Benjamin Schubert, Christopher Mohr',
+      url='https://github.com/FRED-2/OptiType',
+      license='LICENSE',
+      # provided packages
+      packages=['optitype'],
+      # data files required by optitype
+      package_data={'optitype': ['config.ini', 'data/*']},
+      # provided binary packages
+      scripts=['bin/optitype'],
+      # packages that we depend on
+      install_requires=[
+        'Coopr>=3.5,<4.0',
+        'argparse==1.2.1',
+        'biopython==1.65',
+        'matplotlib==1.4.3',
+        'wsgiref==0.1.2',
+        'numpy==1.9.2',
+        'pandas==0.16.2',
+        'tables==3.2.0',
+      ]
+      )