diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py index 6e5a36cd402..cae14ee872d 100644 --- a/var/spack/repos/builtin/packages/abyss/package.py +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/btllib/package.py b/var/spack/repos/builtin/packages/btllib/package.py new file mode 100644 index 00000000000..6eaee0e5f94 --- /dev/null +++ b/var/spack/repos/builtin/packages/btllib/package.py @@ -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"]