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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 UcscBedclip(Package):
"""Remove lines from bed file that refer to off-chromosome locations."""
homepage = "http://hgdownload.cse.ucsc.edu/admin/exe/"
url = "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v449.src.tgz"
maintainers("pabloaledo")
version("377", sha256="932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676")
version("449", sha256="b5a86863d6cfe2120f6c796a13b1572ad05b22622f6534b95c9d26ccbede09b7")
depends_on("libpng")
depends_on("libuuid")
depends_on("gmake")
depends_on("mysql-connector-c")
depends_on("openssl")
depends_on("zlib-api")
def setup_build_environment(self, env):
env.set("MYSQLLIBS", "-lmysqlclient")
env.set("L", "-lssl")
env.set("BINDIR", "bin")
def install(self, spec, prefix):
with working_dir("kent/src/lib"):
make()
with working_dir("kent/src/htslib"):
make()
with working_dir("kent/src/jkOwnLib"):
make()
with working_dir("kent/src/hg/lib"):
make()
with working_dir("kent/src/hg/lib"):
make()
with working_dir("kent/src/utils/bedClip"):
mkdirp("bin")
mkdirp(prefix.bin)
make()
make("install")
install("bin/bedClip", prefix.bin)
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