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add py-gemini (#16950)

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* py-gemini +

* dep py-setuptools +

* deps grabix+

* py-gemini dep version fix

* grabix compiler fix

* Update package.py

Typo correction
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manifest 2020-12-18 04:47:01 +10:30 committed by GitHub
parent a0843e9634
commit 888c456ece
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var/spack/repos/builtin/packages/grabix/package.py Normal file
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# Copyright 2013-2020 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 Grabix(MakefilePackage):
"""Grabix leverages the fantastic BGZF library in samtools to provide
random access into text files that have been compressed with bgzip.
grabix creates it's own index (.gbi) of the bgzipped file. Once indexed,
one can extract arbitrary lines from the file with the grab command.
Or choose random lines with the, well, random command.
"""
homepage = "https://github.com/arq5x/grabix"
url = "https://github.com/arq5x/grabix/archive/v0.1.7.tar.gz"
maintainers = ['robqiao']
version('0.1.7', sha256='d90735c55c0985a4d751858d7ce9e36ad534fff4103257e8e981e34d5c915b28')
conflicts('%gcc@7:', msg='grabix cannot be compiled with newer versions of GCC')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('LICENSE', prefix)
install('simrep.chr1.bed', prefix)
install('grabix', prefix.bin)

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var/spack/repos/builtin/packages/py-gemini/package.py Normal file
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# Copyright 2013-2020 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 PyGemini(PythonPackage):
"""GEMINI (GEnome MINIng) is a flexible framework for exploring genetic
variation in the context of the wealth of genome annotations available
for the human genome.
"""
homepage = "https://gemini.readthedocs.org"
url = "https://github.com/arq5x/gemini/archive/v0.30.2.tar.gz"
maintainers = ['robqiao']
version('0.30.2', sha256='c7af06a4cc475a846aeeb3cd7fcfb39d6cdd0b76e3b07abab2e5e6e68a3fe431')
version('0.30.1', sha256='af835ca33bc6d7865def2467c34cb1d539ec542f9514044435bd2252b25a046d')
version('0.30.0', sha256='a55d0c77342bf650f7e1300cb6ba485407ea3b42f4137a5197248d397a026030')
version('0.20.1', sha256='cd84aa45ace7a9ffb13ba4176122eab5b9fcc0445b1c0944ecec017f88f2b7f1')
version('0.20.0', sha256='640b40186fa00f54c1a0cdfab3fc3076b1d3bdf5c6327fcb2a0c51aa1b05878b')
version('0.19.1', sha256='1154bcb48b1bc78819c5a5e710f5cb0747b01fa0f3113e6081a5a2747c8703e5')
version('0.19.0', sha256='5146d1b5ed52139c50473aa3625d8df29f2db6d198cfd2c966469e7d585cccf2')
version('0.18.3', sha256='7c2f99069385547c656021fbb43e0bae4f9fb8a56ad3f6a61235b44fbc1ba6eb')
version('0.18.2', sha256='cf8a83d48d966a800aa2569076d52c307f4d8264a6ae804c176d61e705c0017e')
version('0.18.1', sha256='1d3d3b9d47555e1f62c1a870d8fd2ecbfc0bed25910cab31af5b585db3144a68')
depends_on('python@2.5:2.8', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('tabix', type=('build', 'run'))
depends_on('grabix', type=('build', 'run'))
depends_on('bedtools2', type=('build', 'run'))
depends_on('py-numpy@1.7.1:', type=('build', 'run'))
depends_on('py-inheritance@0.1.3:', type=('build', 'run'))
depends_on('py-geneimpacts@0.1.3:', type=('build', 'run'))
depends_on('py-cython@0.22.1:', type=('build', 'run'))
depends_on('py-sqlalchemy@1:', type=('build', 'run'))
depends_on('py-pysam@0.6:', type=('build', 'run'))
depends_on('py-cyvcf2@0.7.2:', type=('build', 'run'))
depends_on('py-pyyaml@3.10:', type=('build', 'run'))
depends_on('py-pybedtools@0.6.2:', type=('build', 'run'))
depends_on('py-jinja2@2.7.1:', type=('build', 'run'))
depends_on('py-networkx@1.10:', type=('build', 'run'))
depends_on('py-bottle@0.11.6:', type=('build', 'run'))
depends_on('py-ipyparallel@4.0:', type=('build', 'run'))
depends_on('py-ipython-cluster-helper@0.5.1:', type=('build', 'run'))
depends_on('py-bx-python@0.7.1:', type=('build', 'run'))
depends_on('py-pandas@0.11.0:', type=('build', 'run'))
depends_on('py-openpyxl@1.6.1:1.999', type=('build', 'run'))
depends_on('py-scipy@0.12.0:', type=('build', 'run'))
depends_on('py-unidecode@0.04.14:', type=('build', 'run'))
depends_on('py-cyordereddict@0.2.2', type=('build', 'run'))
depends_on('py-bcolz@0.11.3:', type=('build', 'run'))
depends_on('py-numexpr@2.4.3:', type=('build', 'run'))