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# Copyright 2013-2023 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.package import *
class PyIpyrad(PythonPackage):
"""An interactive toolkit for assembly and analysis of restriction-site
associated genomic data sets (e.g., RAD, ddRAD, GBS) for population
genetic and phylogenetic studies."""
homepage = "https://github.com/dereneaton/ipyrad"
url = "https://github.com/dereneaton/ipyrad/archive/refs/tags/0.9.85.tar.gz"
license("GPL-3.0-only")
version("0.9.90", sha256="8b95aa3bae30da15baba90abb03176932411ff708c54d5e4481b811cceb8a4a8")
version("0.9.85", sha256="17b07466531655db878919e426743ac649cfab2e92c06c4e45f76ee1517633f9")
depends_on("py-setuptools", type="build")
# Dependencies found at
# https://ipyrad.readthedocs.io/en/master/3-installation.html#details-dependencies
depends_on("bedtools2", type=("build", "run"))
depends_on("bwa", type=("build", "run"))
depends_on("muscle", type=("build", "run"))
depends_on("py-notebook", type=("build", "run"))
depends_on("samtools", type=("build", "run"))
depends_on("vsearch", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-pandas", type=("build", "run"))
depends_on("py-h5py", type=("build", "run"))
depends_on("py-numba", type=("build", "run"))
depends_on("py-ipyparallel", type=("build", "run"))
depends_on("py-pysam", type=("build", "run"))
depends_on("py-cutadapt", type=("build", "run"))
depends_on("py-requests", type=("build", "run"))
depends_on("py-future", type=("build", "run"))
def patch(self):
# ipyrad/core/Parallel.py assumes that ipcluster will always be
# in the python root
filter_file(
r"^IPCLUSTER_BIN\s*=.*$",
'IPCLUSTER_BIN = "{}"'.format(self.spec["py-ipyparallel"].prefix.bin.ipcluster),
join_path("ipyrad", "core", "Parallel.py"),
)
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