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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 Salmon(CMakePackage):
"""Salmon is a tool for quantifying the expression of transcripts using
RNA-seq data."""
homepage = "https://combine-lab.github.io/salmon/"
url = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
maintainers("snehring")
version("1.9.0", sha256="450d953a5c43fe63fd745733f478d3fbaf24d926cb52731fd38ee21c4990d613")
version("1.4.0", sha256="6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d")
version("0.14.1", sha256="05289170e69b5f291a8403b40d6b9bff54cc38825e9f721c210192b51a19273e")
version("0.12.0", sha256="91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3")
version("0.9.1", sha256="3a32c28d217f8f0af411c77c04144b1fa4e6fd3c2f676661cc875123e4f53520")
version("0.8.2", sha256="299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91")
variant(
"build_type",
default="RELEASE",
description="CMake build type",
values=("DEBUG", "RELEASE"),
)
# 1.8.0 relies on tbb provided config, earlier versions make
# assumptions about the layout of tbb files that are not true in
# 2021.1 and later
conflicts("intel-tbb@2021.1:", when="@:1.7.0")
conflicts("intel-oneapi-tbb@2021.1:", when="@:1.7.0")
depends_on("tbb")
depends_on(
"boost@1.66.0:"
"+program_options+exception+filesystem+system+chrono+serialization"
"+random+graph+timer+iostreams+math+thread+container",
when="@:0.14.1",
)
depends_on(
"boost@1.72.0:"
"+program_options+exception+filesystem+system+chrono+serialization"
"+random+graph+timer+iostreams+math+thread+container",
when="@1.4.0:",
)
depends_on("cereal")
depends_on("jemalloc")
depends_on("xz")
depends_on("zlib")
depends_on("bzip2")
depends_on("libdivsufsort")
depends_on("staden-io-lib~curl")
depends_on("libgff")
depends_on("pkgconfig")
depends_on("curl", when="@0.14.1:")
conflicts("%gcc@:5.1", when="@0.14.1:")
resources = [
(
"1.9.0",
"pufferfish",
"2a862daeff95a19c9b188bc26a5d02fc0ecc5b9c9ae5523a67c9d14e62551c5d",
),
(
"1.4.0",
"pufferfish",
"059207e8d3134060ed70595e53f4189954c9e5edfaa6361b46304f55d1b71bc7",
),
("0.14.1", "RapMap", "fabac2f360513b803aa3567415eddcd97261ab8a23d4f600af5f98ee8ffd944b"),
("0.12.0", "RapMap", "05102c0bbc8a0c0056a01cd0e8788fa5b504aee58ac226ab8c0e3ffec8019790"),
("0.9.1", "RapMap", "8975e5a1ed61ed9354ba776272927545f417ecdce95823e71ba1e7b61de7d380"),
("0.8.2", "RapMap", "1691f4bca2b604f05f36772ae45faf0842ab4809843df770bd10366a5cfd6822"),
]
for ver, repo, checksum in resources:
resource(
name="rapmap",
url="https://github.com/COMBINE-lab/{0}/archive/salmon-v{1}.zip".format(repo, ver),
sha256=checksum,
placement="external",
expand=False,
when="@{0}".format(ver),
)
def patch(self):
# remove static linking to libstdc++
filter_file("-static-libstdc++", "", "CMakeLists.txt", string=True)
if self.spec.satisfies("@0.8.2:0.9.1"):
filter_file(
"${FAST_MALLOC_LIB}",
"${FAST_MALLOC_LIB}\n" "${CMAKE_DL_LIBS}",
"src/CMakeLists.txt",
string=True,
)
if self.spec.satisfies("@:0.14.1"):
filter_file("curl -k.*", "", "scripts/fetchRapMap.sh")
symlink("./salmon-v{0}.zip".format(self.version), "./external/rapmap.zip")
if self.spec.satisfies("@1.4.0:"):
filter_file("curl -k.*", "", "scripts/fetchPufferfish.sh")
symlink("./salmon-v{0}.zip".format(self.version), "./external/pufferfish.zip")
# Fix issues related to lto-wrapper during install
filter_file(
"INTERPROCEDURAL_OPTIMIZATION True",
"INTERPROCEDURAL_OPTIMIZATION False",
"src/CMakeLists.txt",
string=True,
)
filter_file("curl -k.*", "", "scripts/fetchPufferfish.sh")
def cmake_args(self):
args = ["-DBOOST_ROOT=%s" % self.spec["boost"].prefix]
return args
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