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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 Wise2(MakefilePackage):
"""The Wise2 package is now a rather stately bioinformatics package that
has be around for a while. Its key programs are genewise, a program
for aligning proteins or protein HMMs to DNA, and dynamite a rather
cranky "macro language" which automates the production of dynamic
programming."""
homepage = "https://www.ebi.ac.uk/~birney/wise2/"
url = "https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz"
maintainers("snehring")
version("2.4.1", sha256="240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1")
depends_on("gettext")
depends_on("glib")
depends_on("libiconv")
depends_on("pcre2")
build_directory = "src"
build_targets = ["all"]
def edit(self, spec, prefix):
glib_include_include = join_path(
spec["glib"].prefix.include, "glib-" + str(spec["glib"].version[0]) + ".0"
)
glib_lib_include = join_path(
spec["glib"].prefix.lib, "glib-" + str(spec["glib"].version[0]) + ".0", "include"
)
glib_lib = spec["glib"].prefix.lib
glib_config_files = ["src/makefile", "src/network/makefile", "src/models/makefile"]
for f in glib_config_files:
filter_file(
"`glib-config --cflags`",
f"-I{glib_include_include} -I{glib_lib_include}",
f,
string=True,
)
filter_file("`glib-config --libs`", f"-L{glib_lib} -lglib-2.0", f, string=True)
filter_file('"glib.h"', "<glib.h>", "src/dynlibsrc/subseqhash.h", string=True)
filter_file("getline", "getlineseq", "src/HMMer2/sqio.c", string=True)
filter_file("isnumber", "isdigit", "src/models/phasemodel.c", string=True)
filter_file(r".*welcome.csh.*", "", "src/makefile")
def install(self, spec, prefix):
with working_dir("src"):
install_tree("bin", prefix.bin)
mkdirp(prefix.share.wise2)
install_tree("wisecfg", prefix.share.wise2)
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