
* Bump the package API of the `builtin` repo to `v2.0` * Move `var/spack/repos/builtin` -> `var/spack/repos/spack_repo/builtin` * Move test repos `var/spack/repos/{builtin.mock,tutorial,...}` -> `var/spack/test_repos/` * Update package dir names to v2 format (`-` -> `_` etc) * Change absolute imports `from spack.pkg.builtin.my_pkg ...` to relative imports `from ..my_pkg.package ...` Users who have a repo on top of builtin should change imports from ```python from spack.pkg.builtin.my_pkg import MyPkg ``` to ```python from spack_repo.builtin.packages.my_pkg.package import MyPkg ``` and can configure their editors with ``` PYTHONPATH=$spack/lib/spack:$spack/var/spack/repos ``` [skip-verify-checksums]
66 lines
2.6 KiB
Python
66 lines
2.6 KiB
Python
# Copyright Spack Project Developers. See 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 Shapemapper(CMakePackage):
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"""
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ShapeMapper automates the calculation of RNA structure probing reactivities from mutational
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profiling (MaP) experiments, in which chemical adducts on RNA are detected as internal
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mutations in cDNA through reverse transcription and read out by massively parallel sequencing.
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"""
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homepage = "https://github.com/Weeks-UNC/shapemapper2"
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url = "https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz"
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maintainers("snehring")
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license("MIT")
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version(
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"2.2.0",
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sha256="eec1bfca339731816142bf2e7826dfb2e125588d72a1f7c36aaa927393e6fbec",
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url="https://github.com/Weeks-UNC/shapemapper2/releases/download/2.2.0/shapemapper2-2.2-source-only.tar.gz",
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)
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version(
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"2.1.5",
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sha256="0846a5d8b5f01d2d039fad4b957df0b6220a8505463f1a410368a1b90d2b227c",
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url="https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz",
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)
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depends_on("cxx", type="build") # generated
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depends_on("bowtie2@2.3.0:", type="run", when="@2.1.5")
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depends_on("bowtie2@2.3.4:", type="run", when="@2.2.0:")
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depends_on("perl+threads", type="run")
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depends_on("pv@1.6.20:", type="run")
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# hard version dep due to jni
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depends_on("bbmap@37.78", type="run")
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depends_on("boost+filesystem+program_options+iostreams+system")
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depends_on("star@2.5.2:", type="run")
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depends_on("pv@1.6.0:", type="run")
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depends_on("python@3.7:", type="run", when="@2.1.5")
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depends_on("python@3.9.12:", type="run", when="@2.2.0")
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depends_on("graphviz@2.38.0:", type="run", when="@2.1.5")
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depends_on("graphviz@7.1.0:", type="run", when="@2.2.0:")
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depends_on("py-numpy@1.19.5:1.19", type="run", when="@2.2.0:")
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depends_on("py-scikit-learn@0.18.1:", type="run", when="@2.1.5")
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depends_on("py-scikit-learn@1.1.2:", type="run", when="@2.2.0:")
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depends_on("py-matplotlib@1.5.1:3.3", type="run", when="@2.1.5")
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depends_on("py-matplotlib@3.6.2:3.6", type="run", when="@2.2.0:")
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depends_on("zlib-api")
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build_directory = "build"
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def install(self, spec, prefix):
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for d in ["docs", "internals", "util"]:
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mkdirp(join_path(prefix, d))
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install_tree(d, join_path(prefix, d))
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for f in ["shapemapper", "README.md"]:
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install(f, prefix)
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def setup_run_environment(self, env: EnvironmentModifications) -> None:
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env.prepend_path("PATH", self.prefix)
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