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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)
from spack.package import *
class Repeatmodeler(Package):
"""RepeatModeler is a de-novo repeat family identification and modeling
package."""
homepage = "https://www.repeatmasker.org/RepeatModeler/"
url = "https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.4.tar.gz"
maintainers("snehring")
license("OSL-2.1")
version("2.0.4", sha256="94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6")
version(
"1.0.11",
sha256="7ff0d588b40f9ad5ce78876f3ab8d2332a20f5128f6357413f741bb7fa172193",
url="https://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz",
)
depends_on("perl", type=("build", "run"))
depends_on("perl-json", type=("build", "run"))
depends_on("perl-uri", type=("build", "run"))
depends_on("perl-libwww-perl", type=("build", "run"))
depends_on("perl-file-which", type=("build", "run"), when="@2.0.4:")
depends_on("perl-devel-size", type=("build", "run"), when="@2.0.4:")
depends_on("repeatmasker", type="run")
depends_on("recon+repeatmasker", type="run")
depends_on("repeatscout", type="run")
depends_on("trf", type="run")
depends_on("nseg", type="run")
depends_on("ncbi-rmblastn", type="run")
# "optional" dependencies that it still wants
depends_on("cdhit", type="run", when="@2.0.4:")
depends_on("genometools", type="run", when="@2.0.4:")
depends_on("mafft", type="run", when="@2.0.4:")
depends_on("ninja-phylogeny", type="run", when="@2.0.4:")
depends_on("blat", type="run", when="@2.0.4:")
depends_on("ltr-retriever", type="run", when="@2.0.4:")
def install(self, spec, prefix):
# interactive configuration script
if spec.satisfies("@1.0.11"):
config_answers = [
"",
"",
"",
spec["repeatmasker"].prefix.bin,
spec["recon"].prefix.bin,
spec["repeatscout"].prefix.bin,
spec["nseg"].prefix.bin,
spec["trf"].prefix.bin,
"1",
spec["ncbi-rmblastn"].prefix.bin,
"Y",
"3",
]
elif spec.satisfies("@2.0.4:"):
config_answers = [
"",
spec["repeatmasker"].prefix.bin,
spec["recon"].prefix.bin,
spec["repeatscout"].prefix.bin,
spec["trf"].prefix.bin,
spec["cdhit"].prefix.bin,
spec["blat"].prefix.bin,
spec["ncbi-rmblastn"].prefix.bin,
"y",
spec["genometools"].prefix.bin,
spec["ltr-retriever"].prefix.bin,
spec["mafft"].prefix.bin,
spec["ninja-phylogeny"].prefix.bin,
]
config_filename = "spack-config.in"
with open(config_filename, "w") as f:
f.write("\n".join(config_answers))
with open(config_filename, "r") as f:
perl = which("perl")
perl("configure", input=f)
install_tree(".", prefix.bin)
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