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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 PyPipits(PythonPackage):
"""Automated pipeline for analyses of fungal ITS from the Illumina"""
homepage = "https://github.com/hsgweon/pipits"
url = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz"
version('2.4', sha256='b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054')
version('1.5.0', sha256='6c76fff42a9db62ff4bb1d4d520ebee6cb20d5a726f12c3d5a3d42314947a659', deprecated=True)
# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml
depends_on('python@3:', type=('build', 'run'), when='@2:')
depends_on('python@:2', type=('build', 'run'), when='@:1')
depends_on('py-setuptools', type='build', when='@2:')
depends_on('py-pispino@1.1:', type=('build', 'run'), when='@2:')
depends_on('vsearch', type='run')
depends_on('fastx-toolkit', type='run')
depends_on('hmmer', type='run')
depends_on('itsx', type='run')
depends_on('py-biom-format', type=('build', 'run'))
depends_on('rdptools', type='run', when='@2:')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-pandas', type=('build', 'run'), when='@2:')
depends_on('py-progressbar2', type=('build', 'run'), when='@2:')
depends_on('py-requests', type=('build', 'run'), when='@2:')
depends_on('seqkit', type='run')
depends_on('java', type=('build', 'run'), when='@:1')
depends_on('rdp-classifier', type='run', when='@:1')
resource(
name='UNITE_retrained',
url='http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz',
destination='refdb'
)
resource(
name='uchime_reference_dataset_01.01.2016.fasta',
url='https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip',
destination=join_path('refdb', 'uchime_reference_dataset_01.01.2016')
)
resource(
name='warcup_retrained_V2',
url='https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz',
destination='refdb'
)
@run_after('install')
def install_db(self):
install_tree(join_path(self.stage.source_path, 'refdb'),
self.prefix.refdb)
def setup_run_environment(self, env):
env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path(
self.prefix, 'refdb',
'uchime_reference_dataset_01.01.2016',
'uchime_reference_dataset_01.01.2016.fasta'))
env.set('PIPITS_UNITE_RETRAINED_DIR',
self.prefix.refdb.UNITE_retrained)
env.set('PIPITS_WARCUP_RETRAINED_DIR',
self.prefix.refdb.warcup_retrained_V2)
env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path(
self.spec['rdp-classifier'].prefix.bin,
'classifier.jar'))
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