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# Copyright 2013-2022 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"
version('0.48.0', sha256='1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0')
version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
depends_on('zlib')
depends_on('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:')
# 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(Kallisto, self).std_cmake_args
if (self.spec.version >= Version('0.44.0')):
args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
else:
args = a
return args
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