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abyss: update to use oneapi packages, addv2.3.10 (#49429)

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Add missing btllib dependency, needed from v2.3.6

Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This commit is contained in:
Massimiliano Culpo 2025-03-13 08:56:39 +01:00 committed by GitHub
parent 774346038e
commit 64220779d4
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GPG Key ID: B5690EEEBB952194
2 changed files with 49 additions and 8 deletions
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18
var/spack/repos/builtin/packages/abyss/package.py
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@ -26,6 +26,7 @@ class Abyss(AutotoolsPackage):
homepage = "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
url = "https://github.com/bcgsc/abyss/releases/download/2.3.1/abyss-2.3.1.tar.gz"
version("2.3.10", sha256="bbe42e00d1ebb53ec6afaad07779baaaee994aa5c65b9a38cf4ad2011bb93c65")
version("2.3.7", sha256="ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f")
version("2.3.5", sha256="5455f7708531681ee15ec4fd5620526a53c86d28f959e630dc495f526b7d40f7")
version("2.3.1", sha256="664045e7903e9732411effc38edb9ebb1a0c1b7636c64b3a14a681f465f43677")
@ -35,8 +36,8 @@ class Abyss(AutotoolsPackage):
version("2.0.2", sha256="d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df")
version("1.5.2", sha256="8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1")
depends_on("c", type="build") # generated
depends_on("cxx", type="build") # generated
depends_on("c", type="build")
depends_on("cxx", type="build")
variant(
"maxk", default=128, values=is_multiple_32, description="set the maximum k-mer length."
@ -46,6 +47,8 @@ class Abyss(AutotoolsPackage):
depends_on("automake", type="build")
depends_on("bwa", type="run")
depends_on("btllib", when="@2.3.6:")
depends_on("mpi")
depends_on("boost@:1.50.0,1.53.0:", when="@2.0.2:")
depends_on("boost@:1.50.0,1.53.0:1.59.0", when="@:1.5.2")
@ -55,10 +58,11 @@ class Abyss(AutotoolsPackage):
depends_on("sqlite")
depends_on("libtool")
conflicts("^intel-mpi")
conflicts("^intel-parallel-studio+mpi")
conflicts("^mvapich2")
conflicts("^spectrum-mpi")
conflicts("^[virtuals=mpi] intel-oneapi-mpi")
conflicts("^[virtuals=mpi] mvapich2")
conflicts("^[virtuals=mpi] spectrum-mpi")
patch("fix_BloomFilter.hpp.patch", when="@2.0.0:2.1.4")
def configure_args(self):
maxk = int(self.spec.variants["maxk"].value)
@ -72,5 +76,3 @@ def configure_args(self):
if self.spec["mpi"].name == "mpich":
args.append("--enable-mpich")
return args
patch("fix_BloomFilter.hpp.patch", when="@2.0.0:2.1.4")

39
var/spack/repos/builtin/packages/btllib/package.py Normal file
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@ -0,0 +1,39 @@
# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Btllib(MesonPackage):
"""Bioinformatics Technology Lab common code library in C++
with Python wrappers.
"""
homepage = "https://github.com/bcgsc/btllib"
url = "https://github.com/bcgsc/btllib/releases/download/v1.7.5/btllib-1.7.5.tar.gz"
license("GPL-3.0-or-later")
version("1.7.5", sha256="118a9f8d6445a618178bfbec40d121bbe03014e767261522148f642686090c76")
version("1.7.4", sha256="8c046340b9db4d580521297bfd9cb55af6877a34b48cf6a053266703ebc17837")
depends_on("c", type="build")
depends_on("cxx", type="build")
depends_on("gettext")
with default_args(type="build"):
depends_on("cmake")
depends_on("ninja")
depends_on("python@3.9:")
with default_args(type=("build", "run")):
depends_on("samtools")
depends_on("gzip")
depends_on("xz")
depends_on("bzip2")
depends_on("tar")
depends_on("wget")
def meson_args(self):
return ["-Db_ndebug=true", "-Db_coverage=false"]