From e30a8e70cea8b47a5ebc33d99ac7b87c345b48f6 Mon Sep 17 00:00:00 2001 From: downloadico Date: Fri, 5 Aug 2022 09:12:06 -0600 Subject: [PATCH] seq-gen: add new package (#31916) --- .../repos/builtin/packages/seq-gen/package.py | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 var/spack/repos/builtin/packages/seq-gen/package.py diff --git a/var/spack/repos/builtin/packages/seq-gen/package.py b/var/spack/repos/builtin/packages/seq-gen/package.py new file mode 100644 index 0000000000..19a31b5c11 --- /dev/null +++ b/var/spack/repos/builtin/packages/seq-gen/package.py @@ -0,0 +1,33 @@ +# 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 SeqGen(MakefilePackage): + """Seq-Gen is a program that will simulate the evolution of nucleotide or + amino acid sequences along a phylogeny. + + Seq-Gen is a program that will simulate the evolution of nucleotide or + amino acid sequences along a phylogeny, using common models of the + substitution process. A range of models of molecular evolution are implemented + including the general reversible model. State frequencies and other parameters + of the model may be given and site-specific rate heterogeneity may also be + incorporated in a number of ways. Any number of trees may be read in and the + program will produce any number of data sets for each tree. Thus large sets of + replicate simulations can be easily created. It has been designed to be a + general purpose simulator that incorporates most of the commonly used (and + computationally tractable) models of molecular sequence evolution.""" + + homepage = "http://tree.bio.ed.ac.uk/software/Seq-Gen/" + url = "https://github.com/rambaut/Seq-Gen/archive/refs/tags/1.3.4.tar.gz" + + version("1.3.4", sha256="092ec2255ce656a02b2c3012c32443c7d8e38c692f165fb155b304ca030cbb59") + + build_directory = "source" + + def install(self, spec, prefix): + mkdir(prefix.bin) + install("source/seq-gen", prefix.bin)