From 167c75842aece24304ed093bb169b976f8543836 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Thu, 27 Feb 2020 12:06:19 -0600 Subject: new package: py-cnvkit and py-pomegranate (#15222) The py-pomegranate package is a dependency of py-cnvkit --- .../repos/builtin/packages/py-cnvkit/package.py | 28 ++++++++++++++++++++++ .../builtin/packages/py-pomegranate/package.py | 23 ++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-cnvkit/package.py create mode 100644 var/spack/repos/builtin/packages/py-pomegranate/package.py 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')) -- cgit v1.2.3-60-g2f50