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# 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 Mummer(Package):
"""MUMmer is a system for rapidly aligning entire genomes."""
homepage = "http://mummer.sourceforge.net/"
url = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download"
license("Artistic-1.0")
version("3.23", sha256="1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f")
depends_on("gnuplot")
depends_on("perl", type=("build", "run"))
patch("Makefile.patch")
patch("scripts-Makefile.patch")
def patch(self):
"""Fix mummerplot's use of defined on hashes (deprecated
since perl@5.10, made illegal in perl@5.20."""
kwargs = {"string": True}
filter_file("defined (%", "(%", "scripts/mummerplot.pl", **kwargs)
def install(self, spec, prefix):
if self.run_tests:
make("check")
make("INSTALL_TOP_DIR={0}".format(prefix))
bd = prefix.bin
abd = join_path(prefix, "aux_bin")
sd = join_path(prefix, "scripts")
mkdirp(bd)
mkdirp(abd)
mkdirp(sd)
bins = [
"show-tiling",
"show-snps",
"show-coords",
"show-aligns",
"show-diff",
"delta-filter",
"combineMUMs",
"mummer",
"repeat-match",
"annotate",
"mgaps",
"gaps",
"dnadiff",
"nucmer2xfig",
"run-mummer3",
"mummerplot",
"promer",
"run-mummer1",
"nucmer",
"mapview",
"exact-tandems",
]
aux_bins = ["aux_bin/postnuc", "aux_bin/postpro", "aux_bin/prenuc", "aux_bin/prepro"]
scripts = ["scripts/Foundation.pm"]
for f in bins:
install(f, join_path(bd, f))
for f in aux_bins:
install(f, join_path(abd, f[8:]))
for f in scripts:
install(f, join_path(sd, f[8:]))
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