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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 os
from spack.package import *
class Trf(AutotoolsPackage):
"""Tandem Repeats Finder is a program to locate and display tandem repeats
in DNA sequences.
Note: A manual download is required for TRF.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
https://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://tandem.bu.edu/trf/trf.html"
url = "https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz"
license("AGPL-3.0-only")
version("4.09.1", sha256="516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a")
version("4.09", sha256="9332155384bef82f6c7c449c038d27f1a14b984b2e93000bfcf125f4d44d6aca")
# Beginning with version 4.09, trf is open source and available via github.
# Only version 4.07b needs to be installed as a binary.
manual_download = True
version(
"4.07b",
sha256="a3a760c7b74c9603fbc08d95e8fa696c00f35a2f179b0bd63b2b13757ad3b471",
expand=False,
url="file://{0}/trf407b.linux64".format(os.getcwd()),
deprecated=True,
)
@when("@4.07b")
def autoreconf(self, spec, prefix):
touch("configure")
@when("@4.07b")
def configure(self, spec, prefix):
pass
@when("@4.07b")
def build(self, spec, prefix):
pass
@when("@4.07b")
def install(self, spec, prefix):
mkdirp(prefix.bin)
trfname = "trf{0}.linux64".format(self.version.joined)
install(trfname, prefix.bin)
chmod = which("chmod")
chmod("+x", os.path.join(prefix.bin, trfname))
os.symlink(trfname, prefix.bin.trf)
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