py-whatshap: new package at 0.17 (#10377)

* py-whatshap: new package at 0.17

* py-whatshap: remove unused build_args

var/spack/repos/builtin/packages/py-whatshap/package.py

@@ -0,0 +1,31 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyWhatshap(PythonPackage):
+    """WhatsHap is a software for phasing genomic variants using DNA
+       sequencing reads, also called read-based phasing or haplotype
+       assembly."""
+
+    homepage = "https://whatshap.readthedocs.io/en/latest/"
+    url      = "https://bitbucket.org/whatshap/whatshap/get/v0.17.tar.gz"
+
+    version('0.17', sha256='5f342cbd28f5d3e79490754f067aa67e8bb059da1c042d944b9f75663ef6b055')
+
+    depends_on('python@3.4:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython@0.17:', type=('build', 'run'))
+    depends_on('py-pysam@0.14.0:', type='run')
+    depends_on('py-xopen', type='run')
+    depends_on('py-pyvcf', type='run')
+    depends_on('py-pyfaidx', type='run')
+    depends_on('py-networkx', type='run')
+
+    def patch(self):
+        # there is a stray \xe2 somewhere in setup.py,
+        # explicitly using utf-8 will let the install proceed
+        filter_file('^"""$', '#coding: utf-8\n"""', 'setup.py')