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| -rw-r--r-- | var/spack/repos/builtin/packages/py-ipyrad/package.py | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/py-ipyrad/package.py b/var/spack/repos/builtin/packages/py-ipyrad/package.py new file mode 100644 index 0000000000..1419f75bfa --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ipyrad/package.py @@ -0,0 +1,49 @@ +# 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" + + 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"), + ) |