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liftoff: add new package (#45726)

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Signed-off-by: Shane Nehring <snehring@iastate.edu>
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snehring 2024-08-19 02:48:47 -05:00 committed by GitHub
parent e1ede9c04b
commit 430ba496d1
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3 changed files with 73 additions and 2 deletions
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39
var/spack/repos/builtin/packages/liftoff/package.py Normal file
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@ -0,0 +1,39 @@
# Copyright 2013-2024 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 Liftoff(PythonPackage):
"""Liftoff is a tool that accurately maps annotations in GFF or
GTF between assemblies of the same, or closely-related species.
"""
homepage = "https://github.com/agshumate/Liftoff"
pypi = "liftoff/Liftoff-1.6.3.2.tar.gz"
git = "https://github.com/agshumate/Liftoff.git"
maintainers("snehring")
license("GPL-3.0-only", checked_by="snehring")
version("1.6.3.2", sha256="7070a861144d0f043533893d39f95589a64d63f0365a99d06d71f1700b7fb758")
depends_on("python@3:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-numpy@1.22:", type=("build", "run"))
depends_on("py-biopython@1.76:", type=("build", "run"))
depends_on("py-gffutils@0.10.1:", type=("build", "run"))
depends_on("py-networkx@2.4:", type=("build", "run"))
depends_on("py-pysam@0.19.1:", type=("build", "run"))
depends_on("py-pyfaidx@0.5.8:", type=("build", "run"))
depends_on("py-interlap@0.2.6:", type=("build", "run"))
depends_on("py-ujson@3:", type=("build", "run"))
depends_on("py-parasail@1.2.1:", type=("build", "run"))
depends_on("minimap2", type="run")

21
var/spack/repos/builtin/packages/py-interlap/package.py Normal file
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# Copyright 2013-2024 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 PyInterlap(PythonPackage):
"""interlap: fast, simple interval overlap"""
homepage = "https://brentp.github.io/interlap/index.html"
pypi = "interlap/interlap-0.2.7.tar.gz"
maintainers("snehring")
license("MIT", checked_by="snehring")
version("0.2.7", sha256="31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9")
depends_on("py-setuptools", type="build")

15
var/spack/repos/builtin/packages/py-pyfaidx/package.py
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@ -11,9 +11,20 @@ class PyPyfaidx(PythonPackage):
pypi = "pyfaidx/pyfaidx-0.5.5.2.tar.gz"
maintainers("snehring")
license("BSD-3-Clause")
version("0.8.1.2", sha256="d8452470455b1e778f93969447db8ea24deb4624c7c40769516459cb6f87bc33")
version("0.6.4", sha256="7ba3bdcb1df4ba749f7665b34e6a052aa4e842406a0df95e6df4717cc123f392")
version("0.5.5.2", sha256="9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa")
depends_on("py-setuptools@0.7:", type=("build", "run"))
depends_on("py-six", type=("build", "run"))
depends_on("python@3.7:", type=("build", "run"), when="@0.8.1.2:")
depends_on("py-setuptools@0.7:", type="build")
depends_on("py-setuptools@45:", type="build", when="@0.8.1.2:")
depends_on("py-setuptools-scm", type="build", when="@0.8.1.2:")
depends_on("py-importlib-metadata", type="build", when="@0.8.1.2:")
depends_on("py-packaging", type=("build", "run"), when="@0.8.1.2:")
depends_on("py-six", type=("build", "run"), when="@:0.6.4")