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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 Kallisto(CMakePackage):
"""kallisto is a program for quantifying abundances of transcripts from
RNA-Seq data."""
homepage = "https://pachterlab.github.io/kallisto"
url = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz"
license("BSD-2-Clause")
version("0.48.0", sha256="1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0")
version("0.46.2", sha256="c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2")
version("0.43.1", sha256="7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400")
# HDF5 support is optional beginning with version 0.46.2.
variant("hdf5", when="@0.46.2:", default=False, description="Build with HDF5 support")
depends_on("zlib-api")
depends_on("hdf5", when="@:0.43")
depends_on("hdf5", when="+hdf5")
# htslib isn't built in time to be used....
parallel = False
# v0.44.0 vendored a copy of htslib and uses auto* to build
# its configure script.
depends_on("autoconf", type="build", when="@0.44.0:")
depends_on("automake", type="build", when="@0.44.0:")
depends_on("libtool", type="build", when="@0.44.0:")
depends_on("m4", type="build", when="@0.44.0:")
patch("link_zlib.patch", when="@:0.43")
patch("limits.patch", when="@:0.46")
patch("htslib_configure.patch", when="@0.44.0:^autoconf@2.70:")
@run_before("cmake")
def autoreconf(self):
# Versions of autoconf greater than 2.69 need config.guess and
# config.sub in the tree.
if self.spec.satisfies("@0.44.0:^autoconf@2.70:"):
with working_dir(join_path(self.stage.source_path, "ext", "htslib")):
autoreconf = which("autoreconf")
autoreconf("--install")
# Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
# causes bits of cmake's output to end up in the autoconf-generated
# configure script.
# See https://github.com/spack/spack/issues/15274 and
# https://github.com/pachterlab/kallisto/issues/253
@property
def std_cmake_args(self):
"""Call the original std_cmake_args and then filter the verbose
setting.
"""
a = super().std_cmake_args
if self.spec.satisfies("@0.44.0:"):
args = [i for i in a if i != "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON"]
if self.spec.satisfies("@0.46.2:"):
args.append(self.define_from_variant("USE_HDF5", "hdf5"))
else:
args = a
return args
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