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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)
import glob
from spack.package import *
from spack.pkg.builtin.boost import Boost
class Augustus(MakefilePackage):
"""AUGUSTUS is a program that predicts genes in eukaryotic
genomic sequences"""
homepage = "https://bioinf.uni-greifswald.de/augustus/"
url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
license("Artistic-1.0")
# Releases have moved to github
version("3.5.0", sha256="5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686")
version("3.4.0", sha256="2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8")
version("3.3.2", sha256="d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2")
version(
"3.3.1-tag1",
sha256="011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab",
url="https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz",
)
version(
"3.3",
sha256="b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee",
url="https://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz",
)
version(
"3.2.3",
sha256="a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514",
url="https://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz",
)
depends_on("perl", type=("build", "run"))
depends_on("python", when="@3.3.1:", type=("build", "run"))
depends_on("bamtools")
depends_on("gsl")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("zlib-api")
depends_on("htslib")
depends_on("bcftools")
depends_on("samtools")
depends_on("ncurses")
depends_on("curl", when="@3.3.1:")
depends_on("sqlite", when="@3.4.0:")
depends_on("mysql-client", when="@3.4.0:")
depends_on("mysqlpp", when="@3.4.0:")
depends_on("lp-solve", when="@3.4.0:")
depends_on("suite-sparse", when="@3.4.0:")
# Trying to use filter_file here got too complicated so use a patch with a
# corresponding environment variable
patch("bam2wig_Makefile.patch", when="@3.4.0")
def edit(self, spec, prefix):
# Set compile commands for each compiler and
# Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1)
if "@3.3.1-tag1:3.4.0" in spec:
with working_dir(join_path("auxprogs", "utrrnaseq", "Debug")):
filter_file("g++", spack_cxx, "makefile", string=True)
filter_file(
"g++ -I/usr/include/boost",
f"{spack_cxx} -I{self.spec['boost'].prefix.include}",
"src/subdir.mk",
string=True,
)
# Makefiles to set spack compiler over gcc/g++
makefiles = [
"auxprogs/aln2wig/Makefile",
"auxprogs/bam2hints/Makefile",
"auxprogs/bam2wig/Makefile",
"auxprogs/compileSpliceCands/Makefile",
"auxprogs/homGeneMapping/src/Makefile",
"auxprogs/joingenes/Makefile",
"src/Makefile",
]
if self.version < Version("3.4.0"):
makefiles.append("auxprogs/checkTargetSortedness/Makefile")
if self.version >= Version("3.4.0"):
makefiles.extend(["auxprogs/filterBam/src/Makefile", "src/unittests/Makefile"])
for makefile in makefiles:
filter_file("gcc", spack_cc, makefile, string=True)
filter_file("g++", spack_cxx, makefile, string=True)
bamtools = self.spec["bamtools"].prefix
bcftools = self.spec["bcftools"].prefix
htslib = self.spec["htslib"].prefix
samtools = self.spec["samtools"].prefix
with working_dir(join_path("auxprogs", "filterBam", "src")):
makefile = FileFilter("Makefile")
makefile.filter("BAMTOOLS = .*", f"BAMTOOLS = {bamtools}")
makefile.filter("INCLUDES = *", "INCLUDES = -I$(BAMTOOLS)/include/bamtools ")
if "bamtools@2.5:" in spec:
makefile.filter(
"LIBS = -lbamtools -lz", "LIBS = $(BAMTOOLS)/lib64" "/libbamtools.a -lz"
)
if "bamtools@:2.4" in spec:
makefile.filter(
"LIBS = -lbamtools -lz", "LIBS = $(BAMTOOLS)/lib/bamtools" "/libbamtools.a -lz"
)
with working_dir(join_path("auxprogs", "bam2hints")):
makefile = FileFilter("Makefile")
makefile.filter("/usr/include/bamtools", f"{bamtools}/include/bamtools")
if "bamtools@2.5:" in spec:
makefile.filter(
"LIBS = -lbamtools -lz", f"LIBS = {bamtools}/lib64/libbamtools.a -lz"
)
if "bamtools@:2.4" in spec:
makefile.filter(
"LIBS = -lbamtools -lz", f"LIBS = {bamtools}/lib/bamtools/libbamtools.a -lz"
)
if self.version < Version("3.4.0"):
with working_dir(join_path("auxprogs", "bam2wig")):
makefile = FileFilter("Makefile")
# point tools to spack installations
makefile.filter("BCFTOOLS=.*$", f"BCFTOOLS={bcftools}/include")
makefile.filter("SAMTOOLS=.*$", f"SAMTOOLS={samtools}/include")
makefile.filter("HTSLIB=.*$", f"HTSLIB={htslib}/include")
# fix bad linking dirs
makefile.filter("$(SAMTOOLS)/libbam.a", "$(SAMTOOLS)/../lib/libbam.a", string=True)
makefile.filter("$(HTSLIB)/libhts.a", "$(HTSLIB)/../lib/libhts.a", string=True)
with working_dir(join_path("auxprogs", "checkTargetSortedness")):
makefile = FileFilter("Makefile")
makefile.filter("SAMTOOLS.*=.*$", f"SAMTOOLS={samtools}/include")
makefile.filter("LIBS=-lbam", "LIBS=$(SAMTOOLS)/../lib/libbam.a", string=True)
else:
mysql = self.spec["mysql-client"].prefix
mysqlpp = self.spec["mysqlpp"].prefix
lpsolve = self.spec["lp-solve"].prefix
with working_dir("src"):
makefile = FileFilter("Makefile")
makefile.filter(r"/usr/include/mysql\+\+", f"{mysqlpp}/include/mysql++")
if "^mariadb-c-client" in spec:
makefile.filter("/usr/include/mysql", f"{mysql}/include/mariadb")
else:
makefile.filter("/usr/include/mysql", f"{mysql}/include/mysql")
makefile.filter("/usr/include/lpsolve", f"{lpsolve}/include/lpsolve")
def install(self, spec, prefix):
install_tree("bin", join_path(self.spec.prefix, "bin"))
install_tree("config", join_path(self.spec.prefix, "config"))
install_tree("scripts", join_path(self.spec.prefix, "scripts"))
@run_after("install")
def filter_sbang(self):
with working_dir(self.prefix.scripts):
pattern = "^#!.*"
repl = f"#!{self.spec['perl'].command.path}"
files = glob.glob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
repl = f"#!{self.spec['python'].command.path}"
files = glob.glob("*.py")
for file in files:
filter_file(pattern, repl, *files, backup=False)
def setup_build_environment(self, env):
htslib = self.spec["htslib"].prefix
bamtools = self.spec["bamtools"].prefix
if "@3.4.0" in self.spec:
env.set("HTSLIBDIR", htslib)
if "@3.5.0:" in self.spec:
env.set("HTSLIB_INSTALL_DIR", htslib)
env.set("BAMTOOLS_INSTALL_DIR", bamtools)
def setup_run_environment(self, env):
env.set("AUGUSTUS_CONFIG_PATH", join_path(self.prefix, "config"))
env.prepend_path("PATH", join_path(self.prefix, "scripts"))
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