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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)
from spack.package import *
class Pagit(Package):
"""PAGIT addresses the need for software to generate high quality draft
genomes."""
homepage = "https://www.sanger.ac.uk/science/tools/pagit"
url = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz"
version("1.01", sha256="8069c1d236804cf4ea782495adcc50d18561ef466af06b21946b980b3c37ad55")
depends_on("java", type=("build", "run"))
depends_on("perl", type=("build", "run"))
def install(self, spec, prefix):
with working_dir("PAGIT"):
install_tree("ABACAS", prefix.ABACAS)
install_tree("bin", prefix.bin)
install_tree("ICORN", prefix.ICORN)
install_tree("IMAGE", prefix.IMAGE)
install_tree("lib", prefix.lib)
install_tree("RATT", prefix.RATT)
def setup_run_environment(self, env):
env.set("PAGIT_HOME", self.prefix)
env.set("PILEUP_HOME", join_path(self.prefix.bin, "pileup_v0.5"))
env.set("ICORN_HOME", self.prefix.icorn)
env.set("SNPOMATIC_HOME", self.prefix.bin)
env.set("RATT_HOME", self.prefix.RATT)
env.set("RATT_CONFIG", join_path(self.prefix.RATT, "RATT_config"))
env.prepend_path("PATH", join_path(self.prefix.bin, "pileup_v0.5", "ssaha2"))
env.prepend_path("PATH", join_path(self.prefix.bin, "pileup_v0.5"))
env.prepend_path("PATH", self.prefix.IMAGE)
env.prepend_path("PATH", self.prefix.ABACAS)
env.prepend_path("PATH", self.prefix.ICORN)
env.prepend_path("PATH", self.prefix.RATT)
env.prepend_path("PERL5LIB", self.prefix.lib)
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