From a9c246ed6794cea9b7da40cd703e4e9f4f1a3d39 Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Wed, 29 Jun 2022 08:40:03 -0500 Subject: amrfinder: new package (#31273) --- .../repos/builtin/packages/amrfinder/package.py | 35 ++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 var/spack/repos/builtin/packages/amrfinder/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/amrfinder/package.py b/var/spack/repos/builtin/packages/amrfinder/package.py new file mode 100644 index 0000000000..ce7278293d --- /dev/null +++ b/var/spack/repos/builtin/packages/amrfinder/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2021 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 Amrfinder(MakefilePackage): + """NCBI AMRFinderPlus: This software and the accompanying database identify + acquired antimicrobial resistance genes in bacterial protein and/or + assembled nucleotide sequences as well as known resistance-associated + point mutations for several taxa. With AMRFinderPlus we added select + members of additional classes of genes such as virulence factors, + biocide, heat, acid, and metal resistance genes.""" + + homepage = "https://github.com/ncbi/amr/wiki" + url = "https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v3.10.30.tar.gz" + + version('3.10.30', sha256='2f1e30b86935a27cee740bd7229a41fbce278f2f60b33b8e51592bab8bdf23f1') + version('3.10.24', sha256='fce299c980cda740dcc4f53f9b2dc9061c856213e5bdbc2c339185a5fb7dcf6a') + + depends_on('blast-plus') + depends_on('hmmer') + depends_on('curl') + + def setup_build_environment(self, env): + env.set('INSTALL_DIR', prefix.bin) + env.set('DEFAULT_DB_DIR', prefix.share) + + @run_before('build') + def create_bin_and_share(self): + mkdirp(self.spec.prefix.bin) + mkdirp(self.spec.prefix.share) -- cgit v1.2.3-60-g2f50