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# Copyright 2013-2023 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 *
class Braker(Package):
"""BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
that combines the advantages of GeneMark-ET and AUGUSTUS"""
homepage = "http://exon.gatech.edu/braker1.html"
url = "https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.4.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
license("Artistic-1.0")
version("2.1.6", sha256="eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06")
version("2.1.4", sha256="d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52")
version(
"1.11",
sha256="cb2d9abe1720ed58753d362eee4af3791007efc617754804882d31f9fe2eab00",
url="https://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz",
)
depends_on("perl", type=("build", "run"))
depends_on("perl-scalar-util-numeric", type=("build", "run"))
depends_on("perl-parallel-forkmanager", type=("build", "run"))
depends_on("perl-file-which", type=("build", "run"))
depends_on("perl-yaml", type=("build", "run"))
depends_on("perl-hash-merge", type=("build", "run"))
depends_on("perl-logger-simple", type=("build", "run"))
depends_on("perl-file-homedir", when="@2.1.4:", type=("build", "run"))
depends_on("perl-list-moreutils", when="@2.1.6:", type=("build", "run"))
depends_on("augustus")
depends_on("augustus@3.2.3", when="@:2.1.0")
depends_on("genemark-et")
depends_on("bamtools")
depends_on("samtools")
depends_on("diamond")
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
if self.version < Version("2.1.2"):
install("braker.pl", prefix.bin)
install("filterGenemark.pl", prefix.bin)
install("filterIntronsFindStrand.pl", prefix.bin)
install("helpMod.pm", prefix.lib)
else:
install_tree("docs", prefix.docs)
install_tree("example", prefix.example)
with working_dir("scripts"):
install("helpMod.pm", prefix.lib)
install("*.pl", prefix.bin)
@run_after("install")
def filter_sbang(self):
with working_dir(self.prefix.bin):
pattern = "^#!.*/usr/bin/env perl"
repl = "#!{0}".format(self.spec["perl"].command.path)
files = glob.iglob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
def setup_run_environment(self, env):
env.prepend_path("PERL5LIB", self.prefix.lib)
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