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3 files changed, 79 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/possvm/package.py b/var/spack/repos/builtin/packages/possvm/package.py new file mode 100644 index 0000000000..771256460b --- /dev/null +++ b/var/spack/repos/builtin/packages/possvm/package.py @@ -0,0 +1,47 @@ +# 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) + +import os + +from spack.package import * + + +class Possvm(Package): + """Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL) + is a python tool to analyse pre-computed gene trees and identify pairs + and clusters of orthologous genes. It takes advantage of the species + overlap algorithm implemented in the ETE toolkit to parse the phylogeny + and identify orthologous gene pairs, and MCL clustering for orthogroup + identification.""" + + homepage = "https://github.com/xgrau/possvm-orthology" + git = "https://github.com/xgrau/possvm-orthology.git" + + license("GPL-3.0-only", checked_by="A-N-Other") + + # version number is taken from -v/--version argparse info in possvm.py + version("1.2", commit="3158757423edafc29aa29bf3ae0cc63a93a56df9") + + depends_on("python@3.10:", type="run") + + # dependencies from GitHub README.md + depends_on("py-ete3@3.1.2", type="run") + depends_on("py-markov-clustering@0.0.6.dev0", type="run") + depends_on("py-matplotlib@3.7.1", type="run") + depends_on("py-networkx@3.0", type="run") + depends_on("py-scipy@1.10.0", type="run") + depends_on("py-numpy@1.23.5", type="run") + depends_on("py-pandas@1.5.3", type="run") + + def install(self, spec, prefix): + # This package has no setup.py ... + # Add shebangs, ensure +x, and move the scripts to prefix.bin + mkdirp(prefix.bin) + sed = Executable("sed") + targets = ("possvm.py", join_path("scripts", "possvm_reconstruction.py")) + for script in targets: + sed("-i", rf'1 i\#! {self.spec["python"].command.path}\n', script) + os.chmod(script, 0o755) + install(script, prefix.bin) diff --git a/var/spack/repos/builtin/packages/py-markov-clustering/package.py b/var/spack/repos/builtin/packages/py-markov-clustering/package.py new file mode 100644 index 0000000000..15bc937b01 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-markov-clustering/package.py @@ -0,0 +1,31 @@ +# 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 PyMarkovClustering(PythonPackage): + """Implementation of the Markov clustering (MCL) algorithm in python""" + + homepage = "https://github.com/GuyAllard/markov_clustering" + pypi = "markov_clustering/markov_clustering-0.0.6.dev0.tar.gz" + + license("MIT", checked_by="A-N-Other") + + version( + "0.0.6.dev0", sha256="8f72eee0ee5d9bfbab1b28bbfa95eaa020b2bba64b528ce45030b8b4300ecf33" + ) + + variant("drawing", default=False, description="Include graphing capabilities") + + depends_on("python@3", type=("build", "run")) + depends_on("py-setuptools", type="build") + + depends_on("py-numpy", type=("build", "run")) + depends_on("py-scipy@0.19.0:", type=("build", "run")) + depends_on("py-scikit-learn", type=("build", "run")) + + depends_on("py-networkx", type=("build", "run"), when="+drawing") + depends_on("py-matplotlib", type=("build", "run"), when="+drawing") diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index 693761d3ab..09d123e0a3 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -17,6 +17,7 @@ class PyNetworkx(PythonPackage): license("BSD-3-Clause") version("3.1", sha256="de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61") + version("3.0", sha256="9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412") version("2.8.6", sha256="bd2b7730300860cbd2dafe8e5af89ff5c9a65c3975b352799d87a6238b4301a6") version("2.7.1", sha256="d1194ba753e5eed07cdecd1d23c5cd7a3c772099bd8dbd2fea366788cf4de7ba") version("2.6.3", sha256="c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51") |