py-cnvkit: add new package (#7688)

* py-cnvkit: add new package

* updating dependencies

* correcting flake8 error

* adding py-setuptools dependency

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-cnvkit/package.py b/var/spack/repos/builtin/packages/py-cnvkit/package.py
new file mode 100644
index 0000000000..ed5313f2db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cnvkit/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyCnvkit(PythonPackage):
+    """A command-line toolkit and Python library for detecting copy number
+       variants and alterations genome-wide from high-throughput sequencing."""
+
+    homepage = "http://cnvkit.readthedocs.io/en/stable/"
+    url      = "https://github.com/etal/cnvkit/archive/v0.9.2.tar.gz"
+
+    version('0.9.2', '16612c4dcc9570f6ef9fecc42caf1745')
+
+    depends_on('py-setuptools',        type='build')
+    depends_on('py-biopython@1.62:',   type=('build', 'run'))
+    depends_on('py-future@0.15.2:',    type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
+    depends_on('py-numpy@1.9:',        type=('build', 'run'))
+    depends_on('py-pandas@0.18.1:',    type=('build', 'run'))
+    depends_on('py-pyfaidx@0.4.7:',    type=('build', 'run'))
+    depends_on('py-pysam@0.10.0:',     type=('build', 'run'))
+    depends_on('py-reportlab@3.0:',    type=('build', 'run'))
+    depends_on('py-scipy@0.15.0:',     type=('build', 'run'))