47 lines
2.0 KiB
Python
47 lines
2.0 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Lordec(MakefilePackage):
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"""LoRDEC is a program to correct sequencing errors in long reads from
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3rd generation sequencing with high error rate, and is especially
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intended for PacBio reads."""
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homepage = "http://www.atgc-montpellier.fr/lordec/"
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url = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
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version('0.9', sha256='8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b')
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version('0.8', sha256='3894a7c57649a3545b598f92a48d55eda66d729ab51606b00470c50611b12823')
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def url_for_version(self, version):
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if version == Version('0.8'):
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return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
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if version == Version('0.9'):
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return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/lordec-src_0.9.tar.bz2"
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depends_on('boost@1.48.0:1.64.0', type=['build', 'link'])
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depends_on('gatb-core@1.4.1:', type=['build', 'link', 'run'])
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depends_on('zlib', type=['build', 'link'])
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build_targets = ['clean', 'all']
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def edit(self, spec, prefix):
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lbstr = 'AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no'
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filter_file('^AUTOMATIC_LIBBOOST_LOCAL_INSTALL.*$', lbstr, 'Makefile')
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filter_file('gatb_v.*gatb_core.hpp', '', 'Makefile')
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def install(self, spec, prefix):
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mkdir(prefix.include)
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install('*.h', prefix.include)
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mkdir(prefix.bin)
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binaries = ['lordec-correct', 'lordec-stat', 'lordec-trim',
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'lordec-trim-split', 'lordec-build-SR-graph']
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for binary in binaries:
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install(binary, prefix.bin)
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mkdir(prefix.tools)
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install('lordec_sge_slurm_wrapper.sh', prefix.tools)
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