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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 *
class Repeatmasker(Package):
"""RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences."""
homepage = "https://www.repeatmasker.org"
license("OSL-2.1")
version("4.1.5", sha256="16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f")
version("4.1.2-p1", sha256="4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96")
version("4.0.9", sha256="8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5")
version("4.0.7", sha256="16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166")
variant("crossmatch", description="Enable CrossMatch search engine", default=False)
depends_on("perl", type=("build", "run"))
depends_on("perl-text-soundex", type=("build", "run"))
depends_on("hmmer")
depends_on("ncbi-rmblastn")
depends_on("trf")
depends_on("python", when="@4.1:", type=("build", "run"))
depends_on("py-h5py", when="@4.1:", type=("build", "run"))
depends_on("phrap-crossmatch-swat", type=("build", "run"), when="+crossmatch")
patch("utf8.patch", when="@:4.0")
def url_for_version(self, version):
if version >= Version("4.1.0"):
url = "http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz"
return url.format(version)
else:
url = "http://www.repeatmasker.org/RepeatMasker/RepeatMasker-open-{0}.tar.gz"
return url.format(version.dashed)
def install(self, spec, prefix):
# Config questions consist of:
#
# <PRESS ENTER TO CONTINUE>
# Enter perl path
# Enter where repeatmasker is being configured from
# Enter trf path
# Add a Search Engine:
# 1. CrossMatch
# 2. RMBlast - NCBI Blast with RepeatMasker extensions
# 3. WUBlast/ABBlast (required by DupMasker)
# 4. HMMER3.1 & DFAM
# 5. Done
# Enter RMBlast path
# Do you want RMBlast to be your default search engine for
# Repeatmasker? (Y/N)
# Add a Search Engine: Done
config_answers = []
if spec.satisfies("@:4.0.7"):
# 4.0.9 removes a bunch of the interactive options
config_answers.extend(["", self.spec["perl"].command.path, self.stage.source_path])
# set path to trf
config_answers.append(self.spec["trf"].prefix.bin.trf)
# add crossmatch search
if "+crossmatch" in spec:
crossmatch = self.spec["phrap-crossmatch-swat"].prefix.bin
config_answers.extend(["1", crossmatch, "N"])
# set default BLAST search
config_answers.extend(["2", self.spec["ncbi-rmblastn"].prefix.bin, "Y"])
# set non-default HMMER search
if spec.satisfies("@4.0.9:"):
config_answers.extend(["3", self.spec["hmmer"].prefix.bin, "N"])
else:
config_answers.extend(["4", self.spec["hmmer"].prefix.bin, "N"])
# end configuration
config_answers.append("5")
config_answers_filename = "spack-config.in"
with open(config_answers_filename, "w") as f:
f.write("\n".join(config_answers))
with open(config_answers_filename, "r") as f:
perl = which("perl")
perl("configure", input=f)
# fix perl paths
# every sbang points to perl, so a regex will suffice
for f in glob.glob("*.pm"):
filter_file("#!.*", "#!%s" % spec["perl"].command, f)
install_tree(".", prefix.bin)
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