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kentutils: update to @459, update download location & deps (#42448)

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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This commit is contained in:
George Young 2024-02-05 11:23:33 +00:00 committed by GitHub
parent 1ef52d7c8e
commit 473347df41
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1 changed files with 21 additions and 14 deletions
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35
var/spack/repos/builtin/packages/kentutils/package.py
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@ -9,26 +9,33 @@
class Kentutils(MakefilePackage): class Kentutils(MakefilePackage):
"""Jim Kent command line bioinformatic utilities""" """Jim Kent command line bioinformatic utilities"""
homepage = "https://github.com/ENCODE-DCC/kentUtils" homepage = "https://genome.cse.ucsc.edu/"
git = "https://github.com/ENCODE-DCC/kentUtils.git" url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v453.src.tgz"
version("302.1", commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9") version("459", sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb")
# The above archive only goes back to v305. v302 is left for now but deprecated. Suggest
# this is dropped on next update (v302 is from 2014!) and the `requires()` removed.
version(
"302.1",
commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9",
git="https://github.com/ENCODE-DCC/kentUtils.git",
deprecated=True,
)
depends_on("libpng") depends_on("libpng")
depends_on("openssl") depends_on("openssl")
depends_on("libuuid")
# Actually depends on mysql, but mariadb works for now until mysql is
# available
depends_on("mariadb") depends_on("mariadb")
depends_on("zlib-api")
depends_on("freetype")
depends_on("libiconv")
conflicts("%cce") requires("%gcc", when="@302.1")
conflicts("%apple-clang")
conflicts("%clang") def flag_handler(self, name, flags):
conflicts("%intel") if name == "ldflags":
conflicts("%nag") flags.append(f'{self.spec["libiconv"].libs.ld_flags}')
conflicts("%pgi") return (flags, None, None)
conflicts("%xl")
conflicts("%xl_r")
def install(self, spec, prefix): def install(self, spec, prefix):
install_tree("bin", prefix.bin) install_tree("bin", prefix.bin)