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pharokka and py-phanotate: new packages (#34333)

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* pharokka and py-phanotate: new packages

* move libxcrypt edit

I don't need libxcrypt when not building dev infernal. Moving to a different PR
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Luke Diorio-Toth 2022-12-05 16:16:59 -06:00 committed by GitHub
parent 56072172f5
commit ac1c29eac0
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var/spack/repos/builtin/packages/pharokka/package.py Normal file
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# Copyright 2013-2022 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 Pharokka(Package):
"""pharokka is a rapid standardised annotation
pipeline for bacteriophage genomes"""
homepage = "https://github.com/gbouras13/pharokka"
url = "https://github.com/gbouras13/pharokka/archive/refs/tags/v1.1.0.tar.gz"
version("1.1.0", sha256="57d546f501f201117f5d8037ac47c0d83ccd1ec518080145e8f28d3e9843fba6")
depends_on("py-bcbio-gff", type="run")
depends_on("py-biopython@1.78:", type="run")
depends_on("py-phanotate@1.5.0:", type="run")
depends_on("py-pandas", type="run")
depends_on("mmseqs2@13.45111", type="run")
depends_on("trnascan-se@2.0.9:", type="run")
depends_on("prodigal@2.6.3:", type="run")
depends_on("minced@0.4.2:", type="run")
depends_on("aragorn@1.2.41:", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_tree("bin", prefix.bin)

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# Copyright 2013-2022 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 PyPhanotate(PythonPackage):
"""PHANOTATE is a tool to annotate phage genomes. It uses the assumption
that non-coding bases in a phage genome is disadvantageous, and then
populates a weighted graph to find the optimal path through the six frames
of the DNA where open reading frames are beneficial paths, while gaps and
overlaps are penalized paths."""
homepage = "https://github.com/deprekate/phanotate"
pypi = "phanotate/phanotate-1.5.0.tar.gz"
version("1.5.0", sha256="589e441d2369e5550aef98b8d99fd079d130363bf881a70ac862fc7a8e0d2c88")
depends_on("python@3.5.3:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-fastpath@1.3:", type=("build", "run"))