py-pyani: Create new package (#6811)

1 files changed, 55 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-pyani/package.py b/var/spack/repos/builtin/packages/py-pyani/package.py
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+++ b/var/spack/repos/builtin/packages/py-pyani/package.py
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+##############################################################################
+# Copyright (c) 2013-2017, 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 PyPyani(PythonPackage):
+    """pyani is a Python3 module that provides support for calculating
+    average nucleotide identity (ANI) and related measures for whole genome
+    comparisons, and rendering relevant graphical summary output. Where
+    available, it takes advantage of multicore systems, and can integrate
+    with SGE/OGE-type job schedulers for the sequence comparisons."""
+
+    homepage = "http://widdowquinn.github.io/pyani"
+    url      = "https://pypi.io/packages/source/p/pyani/pyani-0.2.7.tar.gz"
+
+    version('0.2.7', '239ba630d375a81c35b7c60fb9bec6fa')
+    version('0.2.6', 'd5524b9a3c62c36063ed474ea95785c9')
+
+    depends_on('python@3.5:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-seaborn',    type=('build', 'run'))
+
+    # Required for ANI analysis
+    depends_on('py-biopython',  type=('build', 'run'))
+    depends_on('py-pandas',     type=('build', 'run'))
+    depends_on('py-scipy',      type=('build', 'run'))
+
+    # Required for ANIb analysis
+    depends_on('blast-plus~python', type='run')
+
+    # Required for ANIm analysis
+    depends_on('mummer', type='run')