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py-deeptools: new package and dependencies (#4717)

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* py-deeptools: new package and dependencies

* py-deeptools: fixing python things

* missed a fix
This commit is contained in:
Audrey Thoma 2017-07-13 22:02:08 -05:00 committed by Adam J. Stewart
parent 34aea1328a
commit 3eedbd7c4e
5 changed files with 159 additions and 0 deletions
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2
var/spack/repos/builtin/packages/bcftools/package.py
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@ -39,6 +39,8 @@ class Bcftools(Package):
depends_on('zlib')
depends_on('bzip2', when="@1.4:")
# build fails without xz
depends_on('xz', when="@1.4")
def install(self, spec, prefix):
make("prefix=%s" % prefix, "all")

45
var/spack/repos/builtin/packages/py-deeptools/package.py Normal file
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@ -0,0 +1,45 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 PyDeeptools(PythonPackage):
"""deepTools addresses the challenge of handling the large amounts of data
that are now routinely generated from DNA sequencing centers."""
homepage = "https://pypi.io/packages/source/d/deepTools"
url = "https://pypi.io/packages/source/d/deepTools/deepTools-2.5.2.tar.gz"
version('2.5.2', 'ba8a44c128c6bb1ed4ebdb20bf9ae9c2')
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-numpy@1.9.0:', type=('build', 'run'))
depends_on('py-scipy@0.17.0:', type=('build', 'run'))
depends_on('py-py2bit@0.2.0:', type=('build', 'run'))
depends_on('py-pybigwig@0.2.1:', type=('build', 'run'))
depends_on('py-pysam@0.8.2:', type=('build', 'run'))
depends_on('py-matplotlib@1.4.0:', type=('build', 'run'))
depends_on('py-numpydoc@0.5:', type=('build', 'run'))

36
var/spack/repos/builtin/packages/py-py2bit/package.py Normal file
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@ -0,0 +1,36 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 PyPy2bit(PythonPackage):
"""A package for accessing 2bit files using lib2bit."""
homepage = "https://pypi.python.org/pypi/py2bit"
url = "https://pypi.io/packages/source/p/py2bit/py2bit-0.2.1.tar.gz"
version('0.2.1', 'eaf5b1c80a0bbf0b35af1f002f83a556')
depends_on('py-setuptools', type='build')

37
var/spack/repos/builtin/packages/py-pybigwig/package.py Normal file
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@ -0,0 +1,37 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 PyPybigwig(PythonPackage):
"""A package for accessing bigWig files using libBigWig."""
homepage = "https://pypi.python.org/pypi/pyBigWig"
url = "https://pypi.io/packages/source/p/pyBigWig/pyBigWig-0.3.4.tar.gz"
version('0.3.4', '8e0a91e26e87eeaa071408a3a749bfa9')
depends_on('py-setuptools', type='build')
depends_on('curl', type=('build', 'run'))

39
var/spack/repos/builtin/packages/py-pysam/package.py Normal file
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@ -0,0 +1,39 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 PyPysam(PythonPackage):
"""A python module for reading, manipulating and writing genomic data
sets."""
homepage = "https://pypi.python.org/pypi/pysam"
url = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz"
version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.21:', type='build')
depends_on('bcftools')