diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/py-deeptools/package.py | 24 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py | 19 |
2 files changed, 38 insertions, 5 deletions
diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py index bb9be051bc..6c65bb1158 100644 --- a/var/spack/repos/builtin/packages/py-deeptools/package.py +++ b/var/spack/repos/builtin/packages/py-deeptools/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py b/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py new file mode 100644 index 0000000000..bff5b81f69 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py @@ -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') |