c5883fffd7
This PR removes [end of life](https://endoflife.date/python) versions of Python from Spack. Specifically, this includes all versions of Python older than 3.7. See https://github.com/spack/spack/discussions/31824 for rationale. Deprecated in #32615. And #28003. For anyone using software that relies on Python 2, you have a few options: * Upgrade the software to support Python 3. The `3to2` tool may get you most of the way there, although more complex libraries may need manual tweaking. * Add Python 2 as an [external package](https://spack.readthedocs.io/en/latest/build_settings.html#external-packages). Many Python libraries do not support Python 2, but you may be able to add older versions that did once upon a time. * Use Spack 0.19. Spack 0.19 is the last release to officially support Python 3.6 and older * Create and maintain your own [custom repository](https://spack.readthedocs.io/en/latest/repositories.html). Basically, you would need a package for Python 2 and any other Python 2-specific libraries you need.
71 lines
2.6 KiB
Python
71 lines
2.6 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class PyPipits(PythonPackage):
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"""Automated pipeline for analyses of fungal ITS from the Illumina"""
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homepage = "https://github.com/hsgweon/pipits"
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url = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz"
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version("2.4", sha256="b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054")
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# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml
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depends_on("python@3:", type=("build", "run"))
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depends_on("py-setuptools", type="build")
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depends_on("py-pispino@1.1:", type=("build", "run"))
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depends_on("vsearch", type="run")
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depends_on("fastx-toolkit", type="run")
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depends_on("hmmer", type="run")
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depends_on("itsx", type="run")
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depends_on("py-biom-format", type=("build", "run"))
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depends_on("rdptools", type="run")
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depends_on("py-numpy", type=("build", "run"))
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depends_on("py-pandas", type=("build", "run"))
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depends_on("py-progressbar2", type=("build", "run"))
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depends_on("py-requests", type=("build", "run"))
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depends_on("seqkit", type="run")
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resource(
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name="UNITE_retrained",
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url="http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz",
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destination="refdb",
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)
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resource(
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name="uchime_reference_dataset_01.01.2016.fasta",
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url="https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip",
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destination=join_path("refdb", "uchime_reference_dataset_01.01.2016"),
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)
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resource(
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name="warcup_retrained_V2",
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url="https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz",
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destination="refdb",
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)
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@run_after("install")
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def install_db(self):
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install_tree(join_path(self.stage.source_path, "refdb"), self.prefix.refdb)
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def setup_run_environment(self, env):
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env.set(
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"PIPITS_UNITE_REFERENCE_DATA_CHIMERA",
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join_path(
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self.prefix,
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"refdb",
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"uchime_reference_dataset_01.01.2016",
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"uchime_reference_dataset_01.01.2016.fasta",
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),
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)
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env.set("PIPITS_UNITE_RETRAINED_DIR", self.prefix.refdb.UNITE_retrained)
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env.set("PIPITS_WARCUP_RETRAINED_DIR", self.prefix.refdb.warcup_retrained_V2)
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env.set(
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"PIPITS_RDP_CLASSIFIER_JAR",
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join_path(self.spec["rdp-classifier"].prefix.bin, "classifier.jar"),
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)
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