py-pybedtools: Create new package (#6487)

* py-pybedtools: Create new package

* py-pybedtools: add py-six requirement

* py-pybedtools: remove py-cython dependency for release version

* py-pybedtools: include minimum version of py-pysam

1 files changed, 42 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-pybedtools/package.py b/var/spack/repos/builtin/packages/py-pybedtools/package.py
new file mode 100644
index 0000000000..111ba39ee0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pybedtools/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# 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 PyPybedtools(PythonPackage):
+    """pybedtools wraps and extends BEDTools and offers
+    feature-level manipulations from within Python."""
+
+    homepage = "http://daler.github.io/pybedtools"
+    url      = "https://pypi.io/packages/source/p/pybedtools/pybedtools-0.7.10.tar.gz"
+
+    version('0.7.10', 'f003c67e22c48b77f070538368ece70c')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('bedtools2',     type=('build', 'run'))
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-pandas',     type=('build', 'run'))
+    depends_on('py-pysam@0.8.1:', type=('build', 'run'))
+    depends_on('py-six',        type=('build', 'run'))