new package: py-cnvkit and py-pomegranate (#15222)

The py-pomegranate package is a dependency of py-cnvkit

2 files changed, 51 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..17d4508b15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cnvkit/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 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 PyCnvkit(PythonPackage):
+    """Copy number variation toolkit for high-throughput sequencing."""
+
+    homepage = "https://github.com/etal/cnvkit"
+    url      = "https://pypi.io/packages/source/C/CNVkit/CNVkit-0.9.6.tar.gz"
+
+    version('0.9.6', sha256='be889c98a5cf0a994330b8c31c0a65151fb0095fe4e75a1e04118da2516248c2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-futures@3.0:', type=('build', 'run'), when='^python@:2.7')
+    depends_on('py-biopython@1.62:', type=('build', 'run'))
+    depends_on('py-future@0.15.2:', type=('build', 'run'))
+    depends_on('py-pomegranate@0.9.0:', 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@0.20.1:0.24.999', 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'))
diff --git a/var/spack/repos/builtin/packages/py-pomegranate/package.py b/var/spack/repos/builtin/packages/py-pomegranate/package.py
new file mode 100644
index 0000000000..91085ba554
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pomegranate/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 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 PyPomegranate(PythonPackage):
+    """Fast, flexible and easy to use probabilistic modelling in Python."""
+
+    homepage = "https://github.com/jmschrei/pomegranate"
+    url      = "https://pypi.io/packages/source/p/pomegranate/pomegranate-0.12.0.tar.gz"
+
+    version('0.12.0', sha256='8b00c88f7cf9cad8d38ea00ea5274821376fefb217a1128afe6b1fcac54c975a')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython@0.22.1:', type='build')
+    depends_on('py-numpy@1.8.0:', type=('build', 'run'))
+    depends_on('py-joblib@0.9.0b4:', type=('build', 'run'))
+    depends_on('py-networkx@2.0:', type=('build', 'run'))
+    depends_on('py-scipy@0.17.0:', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))