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py-deeptools: add 3.3.0 (#12456)

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Also update dependencies to build latest py-deeptools versions and
add a patch to run tests:

* Replace pypi URL with github URL to download tests
* Update dependency versions of py-pysam, py-matplotlib
* Add new py-deeptoolsintervals package as a dependency
* Add py-plotly and py-nose dependencies
* Patch setup.py to collect and run tests
This commit is contained in:
Pariksheet Nanda
2019-08-21 23:43:44 +00:00
committed by Peter Scheibel
parent 918da9aa55
commit 105da8de02
2 changed files with 38 additions and 5 deletions
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24
var/spack/repos/builtin/packages/py-deeptools/package.py
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@@ -11,10 +11,12 @@ class PyDeeptools(PythonPackage):
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"
# The test suite and associated test data is missing in the pypi tarball.
url = "https://github.com/deeptools/deepTools/archive/3.3.0.tar.gz"
version('3.2.1', sha256='ccbabb46d6c17c927e96fadc43d8d4770efeaf40b9bcba3b94915a211007378e')
version('2.5.2', 'ba8a44c128c6bb1ed4ebdb20bf9ae9c2')
version('3.3.0', sha256='a7aaf79fe939ca307fe6ec5e156750389fdfa4324bf0dd6bf5f53d5fda109358')
version('3.2.1', sha256='dbee7676951a9fdb1b88956fe4a3294c99950ef193ea1e9edfba1ca500bd6a75')
version('2.5.2', sha256='16d0cfed29af37eb3c4cedd9da89b4952591dc1a7cd8ec71fcba87c89c62bf79')
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
@@ -22,6 +24,18 @@ class PyDeeptools(PythonPackage):
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-pysam@0.14.0:', type=('build', 'run'))
depends_on('py-matplotlib@2.1.2:', type=('build', 'run'))
depends_on('py-numpydoc@0.5:', type=('build', 'run'))
depends_on('py-plotly@2.0.0:', type=('build', 'run'))
depends_on('py-deeptoolsintervals@0.1.8:', type=('build', 'run'))
depends_on('py-nose', type='test')
def patch(self):
# Add nosetest hook for "python setup.py test" argument.
filter_file(r'^setup\(',
r'''setup(
tests_require='nose',
test_suite='nose.collector',''',
'setup.py')

19
var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py Normal file
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@@ -0,0 +1,19 @@
# Copyright 2013-2019 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 PyDeeptoolsintervals(PythonPackage):
"""A python module creating/accessing GTF-based interval trees with
associated meta-data."""
homepage = 'https://pypi.org/project/deeptoolsintervals/'
url = 'https://pypi.io/packages/source/d/deeptoolsintervals/deeptoolsintervals-0.1.9.tar.gz'
version('0.1.9', sha256='7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6')
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-setuptools', type='build')