From ac1c29eac036b19dab82a8ec8c8ff54acc2fac78 Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Mon, 5 Dec 2022 16:16:59 -0600 Subject: pharokka and py-phanotate: new packages (#34333) * pharokka and py-phanotate: new packages * move libxcrypt edit I don't need libxcrypt when not building dev infernal. Moving to a different PR --- .../repos/builtin/packages/pharokka/package.py | 31 ++++++++++++++++++++++ .../repos/builtin/packages/py-phanotate/package.py | 24 +++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 var/spack/repos/builtin/packages/pharokka/package.py create mode 100644 var/spack/repos/builtin/packages/py-phanotate/package.py diff --git a/var/spack/repos/builtin/packages/pharokka/package.py b/var/spack/repos/builtin/packages/pharokka/package.py new file mode 100644 index 0000000000..11653ee96c --- /dev/null +++ b/var/spack/repos/builtin/packages/pharokka/package.py @@ -0,0 +1,31 @@ +# 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) diff --git a/var/spack/repos/builtin/packages/py-phanotate/package.py b/var/spack/repos/builtin/packages/py-phanotate/package.py new file mode 100644 index 0000000000..fdea8cb3b2 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-phanotate/package.py @@ -0,0 +1,24 @@ +# 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")) -- cgit v1.2.3-70-g09d2