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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 import *
class Hal(MakefilePackage):
"""HAL is a structure to efficiently store and index multiple
genome alignments and ancestral reconstructions.
HAL is a graph-based representation which provides several advantages
over matrix/block-based formats such as MAF, such as
improved scalability and the ability to perform queries with
respect to an arbitrary reference or subtree."""
homepage = "https://github.com/ComparativeGenomicsToolkit/hal"
url = "https://github.com/ComparativeGenomicsToolkit/hal/archive/release-V2.1.tar.gz"
version('2.1', '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5')
maintainers = ['ilbiondo']
# HAL expects to be compiled alongside sonlib so we need both the
# source version and python library version
depends_on('hdf5+cxx~mpi')
depends_on('sonlib', type='build')
depends_on('python', type='run')
depends_on('py-sonlib', type='run')
# As we install sonlib seperately the include.mk needs
# editing to comment out an include
def patch(self):
includemk = FileFilter('include.mk')
includemk.filter(r'^include \$\{sonLibRootDir\}/include\.mk',
'# include ${sonLibRootDir}/include.mk')
def setup_build_environment(self, env):
env.set('sonLibRootDir', self.spec['sonlib'].prefix)
def install(self, spec, prefix):
# First the easy bit
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)
# Copy the rest of the "toolkit" as to a directory named hal
# in order that the python libraries can be found and used
haldirs = ['alignmentDepth',
'analysis',
'api',
'assemblyHub',
'benchmarks',
'blockViz',
'doc',
'extra',
'extract',
'fasta',
'liftover',
'lod',
'maf',
'modify',
'mutations',
'objs',
'phyloP',
'randgen',
'stats',
'synteny',
'testdata',
'validate']
for folder in haldirs:
install_tree(folder, join_path(self.prefix, 'hal', folder))
install('__init__.py', join_path(self.prefix, 'hal'))
# Now in order to make things useful we copy some python tools to bin
halpyfiles = ['analysis/halContiguousRegions.py',
'assemblyHub/hal2assemblyHub.py',
'liftover/halLiftoverStatus.py',
'lod/halLodBenchmark.py',
'lod/halLodInterpolate.py',
'maf/hal2mafMP.py',
'phyloP/halPhyloPMP.py']
for pyfile in halpyfiles:
install(pyfile, self.prefix.bin)
# The hal directory is a python library so we set the path
# to be the installation root
def setup_run_environment(self, env):
env.prepend_path('PYTHONPATH', self.prefix)
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