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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 os import chmod
from spack.package import *
class Mirdeep2(Package):
"""miRDeep2 is a completely overhauled tool which discovers microRNA genes
by analyzing sequenced RNAs."""
homepage = "https://www.mdc-berlin.de/8551903/en/"
url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
version("0.0.8", sha256="eeb24ee1b0e76b49ee2f542da3ee7d46d163c80b152709e963492b79f4fca1b8")
depends_on("perl", type=("build", "run"))
depends_on("perl-pdf-api2", type=("build", "run"))
depends_on("bowtie")
depends_on("viennarna")
depends_on("squid")
depends_on("randfold")
def url_for_version(self, version):
url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip"
return url.format(version.underscored)
def patch(self):
with working_dir("src"):
files = glob.iglob("*.pl")
for file in files:
chmod(file, 0o755)
change = FileFilter(file)
change.filter("usr/bin/perl", "usr/bin/env perl")
change.filter("perl -W", "perl")
change.filter("../Rfam_for_miRDeep.fa", "Rfam_for_miRDeep.fa")
change.filter("../install_successful", "install_successful")
def install(self, spec, prefix):
install_tree("src", prefix.bin)
install("Rfam_for_miRDeep.fa", prefix.bin)
# miRDeep looks for the install_sucessful file to check if you used
# their automated install script which we'll just be kind of hacking
# around
touch(prefix.bin.install_successful)
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