81 lines
3.2 KiB
Python
81 lines
3.2 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyPipits(PythonPackage):
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"""Automated pipeline for analyses of fungal ITS from the Illumina"""
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homepage = "https://github.com/hsgweon/pipits"
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url = "https://github.com/hsgweon/pipits/archive/1.5.0.tar.gz"
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version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a')
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depends_on('python@:2.999', type=('build', 'run'))
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depends_on('py-biom-format', type=('build', 'run'))
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depends_on('py-numpy', type=('build', 'run'))
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depends_on('java', type=('build', 'run'))
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depends_on('hmmer')
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depends_on('fastx-toolkit')
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depends_on('vsearch')
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depends_on('itsx')
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depends_on('rdp-classifier')
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resource(
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name='UNITE_retrained',
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url='http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz',
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destination='refdb'
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)
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resource(
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name='uchime_reference_dataset_01.01.2016.fasta',
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url='https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip',
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destination=join_path('refdb', 'uchime_reference_dataset_01.01.2016')
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)
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resource(
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name='warcup_retrained_V2',
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url='https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz',
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destination='refdb'
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)
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@run_after('install')
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def install_db(self):
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install_tree(join_path(self.stage.source_path, 'refdb'),
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self.prefix.refdb)
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def setup_environment(self, spack_env, run_env):
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run_env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path(
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self.prefix, 'refdb',
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'uchime_reference_dataset_01.01.2016',
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'uchime_reference_dataset_01.01.2016.fasta'))
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run_env.set('PIPITS_UNITE_RETRAINED_DIR',
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self.prefix.refdb.UNITE_retrained)
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run_env.set('PIPITS_WARCUP_RETRAINED_DIR',
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self.prefix.refdb.warcup_retrained_V2)
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run_env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path(
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self.spec['rdp-classifier'].prefix.bin,
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'classifier.jar'))
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